Citrus Sinensis ID: 046621

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210---
Protein Sequence
MSNEAFDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRKGSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGSRGQGLKDEMLGKNPPPVPASNGRSSNPIKIVKRDANSVRIKLAVGALPEKILTAFQSVLDEHPNEEVALNNCNAAVHHAGKVSEDVENTPSQ
Secondary Structure (PSIPRED)
cccccccHHHHHHHHHcccccHHHHHHHHHHHHHcHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHccccccccHHHHHHHHcccccccccccccccccccccccccccHHHHHHHccccHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHcccc
Secondary Structure Prediction (SSPRO)
cccccccHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHccccccccHccccccccccccccccccccccccccccHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHcccccc
Coil and Loop (DISEMBL)
msneafdgQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQnsrrkgseFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERkvfgsrgqglkdemlgknpppvpasngrssnpikivkrDANSVRIKLAVGALPEKILTAFQSVldehpneevalnncnAAVHhagkvsedventpsq
Flexible Loop (DISEMBL)
msneafdgQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVetwdksfnssqKEQRVSFLYLANDILQNSRRKGSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFgsrgqglkdemlgknpppvpasngrssnpikivkrdaNSVRIKLAVGALPEKILTAFQSVLDEHPNEEVALNNCNAAVHHAgkvsedventpsq
Low Complexity Region (SEG)
MSNEAFDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRKGSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGSRGQGLKDEMLGKNPPPVPASNGRSSNPIKIVKRDANSVRIKLAVGALPEKILTAFQSVLDEHPNEEVALNNCNAAVHHAGKVSEDVENTPSQ
Disordered region (IsUnstruct)
***************************LSRWCITHRKKAKQIVETWDKSF******QRVSFLYLANDILQNSRRKGSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFG******************************IVKRDANSVRIKLAVGALPEKILTAFQSVLDEHPNEEVALNNCNAAV****************
Disordered Region (DISOPRED)
****AFDGQILSEKLSKLNN*QQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRKGSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGSRGQGL********************************************************************A******KV***VE*****
Disordered Region (DISEMBL)
********QILSEKLSK*********SLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRKGSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGSRGQGLKDEMLGKNPPPVPASNGRSSNPIKIVKRDANSVRIKLAVGALPEKILTAFQSVLDEHPNEEVALNNCNAAVHHAGK***********
Disordered Region (DISPRO)
*****FDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRKGSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGSRGQGLKDEMLGK*********************************ALPEKILTAFQSVLDEHPNEEVALNNCNAAVHHAGKVSEDVEN*P**
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSNEAFDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRKGSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGSRGQGLKDEMLGKNPPPVPASNGRSSNPIKIVKRDANSVRIKLAVGALPEKILTAFQSVLDEHPNEEVALNNCNAAVHHAGKVSEDVENTPSQ
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	213	2.2.26 [Sep-21-2011]
Q9CSU0	326	Regulation of nuclear pre	yes	no	0.661	0.432	0.461	2e-28
Q9NQG5	326	Regulation of nuclear pre	yes	no	0.624	0.407	0.474	4e-28
Q5R8Y3	312	Regulation of nuclear pre	no	no	0.619	0.423	0.436	2e-26
Q96P16	312	Regulation of nuclear pre	no	no	0.619	0.423	0.436	2e-26
Q0P5J9	312	Regulation of nuclear pre	no	no	0.619	0.423	0.436	2e-26
Q8VDS4	312	Regulation of nuclear pre	no	no	0.539	0.368	0.469	3e-26
Q5ZM30	268	Regulation of nuclear pre	no	no	0.539	0.429	0.469	3e-25
A8WLG6	311	CID domain-containing pro	N/A	no	0.741	0.508	0.272	7e-15
Q5VT52	1461	Regulation of nuclear pre	no	no	0.497	0.072	0.381	2e-13
Q6NXI6	1469	Regulation of nuclear pre	no	no	0.497	0.072	0.372	2e-13

>sp|Q9CSU0|RPR1B_MOUSE Regulation of nuclear pre-mRNA domain-containing protein 1B OS=Mus musculus GN=Rprd1b PE=1 SV=2

 Score =  125 bits (315), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 66/143 (46%), Positives = 90/143 (62%), Gaps = 2/143 (1%)

Query: 5   AFDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYL 64
           +F    L +KLS+L+NSQQS+++LS W I HRK A  IV  W +    ++  ++++FLYL
Sbjct: 3   SFSESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLYL 62

Query: 65  ANDILQNSRRKGSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGSRG- 123
           AND++QNS+RKG EF  EF  VL  A  HV    DE  KK + RL++IW+ER V+G    
Sbjct: 63  ANDVIQNSKRKGPEFTREFESVLVDAFSHVAREADEGCKKPLERLLNIWQERSVYGGEFI 122

Query: 124 QGLKDEML-GKNPPPVPASNGRS 145
           Q LK  M   K+PPP  A   +S
Sbjct: 123 QQLKLSMEDSKSPPPKAAEEKKS 145

Interacts with phosphorylated C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit POLR2A, and participates in dephosphorylation of the CTD. Transcriptional regulator which enhances expression of CCND1. Promotes binding of RNA polymerase II to the CCDN1 promoter and to the termination region before the poly-A site but decreases its binding after the poly-A site. Prevents RNA polymerase II from reading through the 3' end termination site and may allow it to be recruited back to the promoter through promotion of the formation of a chromatin loop. Also enhances the transcription of a number of other cell cycle-related genes including CDK2, CDK4, CDK6 and cyclin-E but not CDKN1A, CDKN1B or cyclin-A. Promotes cell proliferation.
Mus musculus (taxid: 10090)

>sp|Q9NQG5|RPR1B_HUMAN Regulation of nuclear pre-mRNA domain-containing protein 1B OS=Homo sapiens GN=RPRD1B PE=1 SV=1

 Score =  124 bits (311), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 64/135 (47%), Positives = 87/135 (64%), Gaps = 2/135 (1%)

Query: 5   AFDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYL 64
           +F    L +KLS+L+NSQQS+++LS W I HRK A  IV  W +    ++  ++++FLYL
Sbjct: 3   SFSESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLYL 62

Query: 65  ANDILQNSRRKGSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGSRG- 123
           AND++QNS+RKG EF  EF  VL  A  HV    DE  KK + RL++IW+ER V+G    
Sbjct: 63  ANDVIQNSKRKGPEFTREFESVLVDAFSHVAREADEGCKKPLERLLNIWQERSVYGGEFI 122

Query: 124 QGLKDEML-GKNPPP 137
           Q LK  M   K+PPP
Sbjct: 123 QQLKLSMEDSKSPPP 137

Interacts with phosphorylated C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit POLR2A, and participates in dephosphorylation of the CTD. Transcriptional regulator which enhances expression of CCND1. Promotes binding of RNA polymerase II to the CCDN1 promoter and to the termination region before the poly-A site but decreases its binding after the poly-A site. Prevents RNA polymerase II from reading through the 3' end termination site and may allow it to be recruited back to the promoter through promotion of the formation of a chromatin loop. Also enhances the transcription of a number of other cell cycle-related genes including CDK2, CDK4, CDK6 and cyclin-E but not CDKN1A, CDKN1B or cyclin-A. Promotes cell proliferation.

Homo sapiens (taxid: 9606)

>sp|Q5R8Y3|RPR1A_PONAB Regulation of nuclear pre-mRNA domain-containing protein 1A OS=Pongo abelii GN=RPRD1A PE=2 SV=1

 Score =  119 bits (297), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 58/133 (43%), Positives = 85/133 (63%), Gaps = 1/133 (0%)

Query: 5   AFDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYL 64
           AF    L +KLS+L+NSQQS+++LS W I HRK ++ IV  W++    ++  ++++FLYL
Sbjct: 3   AFSEAALEKKLSELSNSQQSVQTLSLWLIHHRKHSRPIVTVWERELRKAKPNRKLTFLYL 62

Query: 65  ANDILQNSRRKGSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVF-GSRG 123
           AND++QNS+RKG EF  +F  V+  A KHV    DE  KK + R++ IWEER V+     
Sbjct: 63  ANDVIQNSKRKGPEFTKDFAPVIVEAFKHVSSETDESCKKHLGRVLSIWEERSVYENDVL 122

Query: 124 QGLKDEMLGKNPP 136
           + LK  + G   P
Sbjct: 123 EQLKQALYGDKKP 135

Interacts with phosphorylated C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit POLR2A, and participates in dephosphorylation of the CTD. May act as a negative regulator of cyclin-D1 (CCND1) and cyclin-E (CCNE1) in the cell cycle.

Pongo abelii (taxid: 9601)

>sp|Q96P16|RPR1A_HUMAN Regulation of nuclear pre-mRNA domain-containing protein 1A OS=Homo sapiens GN=RPRD1A PE=1 SV=1

 Score =  119 bits (297), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 58/133 (43%), Positives = 85/133 (63%), Gaps = 1/133 (0%)

Query: 5   AFDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYL 64
           AF    L +KLS+L+NSQQS+++LS W I HRK ++ IV  W++    ++  ++++FLYL
Sbjct: 3   AFSEAALEKKLSELSNSQQSVQTLSLWLIHHRKHSRPIVTVWERELRKAKPNRKLTFLYL 62

Query: 65  ANDILQNSRRKGSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVF-GSRG 123
           AND++QNS+RKG EF  +F  V+  A KHV    DE  KK + R++ IWEER V+     
Sbjct: 63  ANDVIQNSKRKGPEFTKDFAPVIVEAFKHVSSETDESCKKHLGRVLSIWEERSVYENDVL 122

Query: 124 QGLKDEMLGKNPP 136
           + LK  + G   P
Sbjct: 123 EQLKQALYGDKKP 135

Interacts with phosphorylated C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit POLR2A, and participates in dephosphorylation of the CTD. May act as a negative regulator of cyclin-D1 (CCND1) and cyclin-E (CCNE1) in the cell cycle.

Homo sapiens (taxid: 9606)

>sp|Q0P5J9|RPR1A_BOVIN Regulation of nuclear pre-mRNA domain-containing protein 1A OS=Bos taurus GN=RPRD1A PE=2 SV=2

 Score =  119 bits (297), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 58/133 (43%), Positives = 85/133 (63%), Gaps = 1/133 (0%)

Query: 5   AFDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYL 64
           AF    L +KLS+L+NSQQS+++LS W I HRK ++ IV  W++    ++  ++++FLYL
Sbjct: 3   AFSEAALEKKLSELSNSQQSVQTLSLWLIHHRKHSRPIVTVWERELRKAKPNRKLTFLYL 62

Query: 65  ANDILQNSRRKGSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVF-GSRG 123
           AND++QNS+RKG EF  +F  V+  A KHV    DE  KK + R++ IWEER V+     
Sbjct: 63  ANDVIQNSKRKGPEFTKDFAPVIVEAFKHVSSETDESCKKHLGRVLSIWEERSVYENDVL 122

Query: 124 QGLKDEMLGKNPP 136
           + LK  + G   P
Sbjct: 123 EQLKQALYGDKKP 135

Interacts with phosphorylated C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit POLR2A, and participates in dephosphorylation of the CTD. May act as a negative regulator of cyclin-D1 (CCND1) and cyclin-E (CCNE1) in the cell cycle.

Bos taurus (taxid: 9913)

>sp|Q8VDS4|RPR1A_MOUSE Regulation of nuclear pre-mRNA domain-containing protein 1A OS=Mus musculus GN=Rprd1a PE=2 SV=1

 Score =  118 bits (295), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 54/115 (46%), Positives = 79/115 (68%)

Query: 5   AFDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYL 64
           AF    L +KLS+L+NSQQS+++LS W I HRK ++ IV  W++    ++  ++++FLYL
Sbjct: 3   AFSEAALEKKLSELSNSQQSVQTLSLWLIHHRKHSRPIVTVWERELRKAKPNRKLTFLYL 62

Query: 65  ANDILQNSRRKGSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVF 119
           AND++QNS+RKG EF  +F  V+  A KHV    DE  KK + R++ IWEER V+
Sbjct: 63  ANDVIQNSKRKGPEFTKDFAPVIVEAFKHVSSETDESCKKHLGRVLSIWEERSVY 117

Interacts with phosphorylated C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit POLR2A, and participates in dephosphorylation of the CTD. May act as a negative regulator of cyclin-D1 (CCND1) and cyclin-E (CCNE1) in the cell cycle.

Mus musculus (taxid: 10090)

>sp|Q5ZM30|RPR1A_CHICK Regulation of nuclear pre-mRNA domain-containing protein 1A OS=Gallus gallus GN=RPRD1A PE=2 SV=1

 Score =  114 bits (286), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 54/115 (46%), Positives = 76/115 (66%)

Query: 5   AFDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYL 64
           AF    L  KLS+L+NSQQS+++LS W I HRK +  IV  W++    ++  ++++FLYL
Sbjct: 3   AFSEAALERKLSELSNSQQSVQTLSLWLIHHRKHSALIVSVWERELRKAKPNRKLTFLYL 62

Query: 65  ANDILQNSRRKGSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVF 119
           AND++QNS+RKG EF  +F  V+  A KHV    DE  KK   R++ IWEER V+
Sbjct: 63  ANDVIQNSKRKGPEFTKDFAPVIVEAFKHVSSESDESCKKHPGRVLSIWEERSVY 117

Gallus gallus (taxid: 9031)

>sp|A8WLG6|CIDS1_CAEBR CID domain-containing protein 1 OS=Caenorhabditis briggsae GN=cids-1 PE=4 SV=1

 Score = 80.5 bits (197), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 46/169 (27%), Positives = 94/169 (55%), Gaps = 11/169 (6%)

Query: 6   FDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRV-SFLYL 64
           F  Q L +KL+ L+N   SI++ S W + +    + I+  W K+     K  +V + LY+
Sbjct: 4   FTEQTLRQKLANLSNHSNSIQTTSSWLLKNHNNREIIIRVWLKTVRKENKGAKVVNLLYV 63

Query: 65  ANDILQNSRRKGSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFG-SRG 123
           AND+ QN+R+   +F ++F+  + +A +H  +   +  + A+ +L+ +W+ER+++  S+ 
Sbjct: 64  ANDVAQNARKACPQFKDDFFPAIESAFRHCCELKAKEVENAIGKLIHVWKERQIYSQSQC 123

Query: 124 QGLKD-----EMLGKNPPPVPASNGRSSNPIKIV----KRDANSVRIKL 163
           + L++     ++ G  P P   +NG++S P + +    K++A  V + L
Sbjct: 124 KRLQEAHQQMKLSGSFPSPAGRNNGKNSQPNQFIVEEAKKNAQDVLVSL 172

Caenorhabditis briggsae (taxid: 6238)

>sp|Q5VT52|RPRD2_HUMAN Regulation of nuclear pre-mRNA domain-containing protein 2 OS=Homo sapiens GN=RPRD2 PE=1 SV=1

 Score = 75.9 bits (185), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 42/110 (38%), Positives = 58/110 (52%), Gaps = 4/110 (3%)

Query: 11  LSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQ 70
           L  K   + N+ +SI+ LS WCI ++K    IV  W K    S    R++  YLAND++Q
Sbjct: 27  LDRKFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSAYPHRLNLFYLANDVIQ 86

Query: 71  NSRRKGSEFVNE-FWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVF 119
           N +RK +    E F  VLP A   V D       K+V R+  IWE+R V+
Sbjct: 87  NCKRKNAIIFRESFADVLPEAAALVKDPS---VSKSVERIFKIWEDRNVY 133

Homo sapiens (taxid: 9606)

>sp|Q6NXI6|RPRD2_MOUSE Regulation of nuclear pre-mRNA domain-containing protein 2 OS=Mus musculus GN=Rprd2 PE=1 SV=1

 Score = 75.9 bits (185), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 41/110 (37%), Positives = 58/110 (52%), Gaps = 4/110 (3%)

Query: 11  LSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQ 70
           L  K   + N+ +SI+ LS WCI ++K    IV  W K    S    R++  YLAND++Q
Sbjct: 27  LDRKFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSTYPHRLNLFYLANDVIQ 86

Query: 71  NSRRKGSEFVNE-FWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVF 119
           N +RK +    E F  VLP A   V D       K++ R+  IWE+R V+
Sbjct: 87  NCKRKNAIIFRESFADVLPEAAALVKDPSV---SKSIERIFKIWEDRNVY 133

Mus musculus (taxid: 10090)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	213
449437658	560	PREDICTED: uncharacterized protein LOC10	0.971	0.369	0.822	6e-99
225439137	562	PREDICTED: uncharacterized protein LOC10	0.981	0.371	0.814	1e-97
296085856	304	unnamed protein product [Vitis vinifera]	0.995	0.697	0.802	3e-97
356506176	523	PREDICTED: uncharacterized protein LOC10	0.995	0.405	0.812	6e-97
255580264	563	conserved hypothetical protein [Ricinus	0.981	0.371	0.765	4e-93
357508995	537	Regulation of nuclear pre-mRNA domain-co	1.0	0.396	0.733	7e-90
255635643	195	unknown [Glycine max]	0.845	0.923	0.834	1e-82
357497311	277	Regulation of nuclear pre-mRNA domain-co	0.962	0.740	0.713	1e-80
356514068	670	PREDICTED: uncharacterized protein LOC10	0.873	0.277	0.759	3e-79
147828708	862	hypothetical protein VITISV_012976 [Viti	0.887	0.219	0.672	7e-78

>gi|449437658|ref|XP_004136608.1| PREDICTED: uncharacterized protein LOC101211730 [Cucumis sativus]

 Score =  365 bits (937), Expect = 6e-99,   Method: Compositional matrix adjust.
 Identities = 172/209 (82%), Positives = 192/209 (91%), Gaps = 2/209 (0%)

Query: 1   MSNEAFDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVS 60
           M+NE F+ Q+L+EKLSKLNNSQQSIESLS+WCI+HRKKAKQIVETWDK FNSSQKEQRVS
Sbjct: 1   MNNEVFEAQVLAEKLSKLNNSQQSIESLSKWCISHRKKAKQIVETWDKLFNSSQKEQRVS 60

Query: 61  FLYLANDILQNSRRKGSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFG 120
           FLYLANDILQNSRRKGSEFVNEFWKVLP ALK+VYD+GDE GKKAV RLV+IWEERKVFG
Sbjct: 61  FLYLANDILQNSRRKGSEFVNEFWKVLPGALKYVYDHGDESGKKAVARLVNIWEERKVFG 120

Query: 121 SRGQGLKDEMLGKNPP--PVPASNGRSSNPIKIVKRDANSVRIKLAVGALPEKILTAFQS 178
           SRGQ LKDEMLGKNPP  P+P+SNG+SSNPIKIVKRDA+SVRIKLAVG +PEKILTAFQS
Sbjct: 121 SRGQSLKDEMLGKNPPPTPLPSSNGKSSNPIKIVKRDAHSVRIKLAVGGVPEKILTAFQS 180

Query: 179 VLDEHPNEEVALNNCNAAVHHAGKVSEDV 207
           VLDEH NE+ AL NC++A HH  ++ ED+
Sbjct: 181 VLDEHLNEDAALINCSSATHHLNQIEEDL 209

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225439137|ref|XP_002267006.1| PREDICTED: uncharacterized protein LOC100250127 [Vitis vinifera]

 Score =  361 bits (926), Expect = 1e-97,   Method: Compositional matrix adjust.
 Identities = 171/210 (81%), Positives = 187/210 (89%), Gaps = 1/210 (0%)

Query: 1   MSNEAFDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVS 60
           MSN+ FDGQ+L+EKLSKLNNSQQSIESLSRWCI+HRKKAKQIVETWDK FNSSQKEQ VS
Sbjct: 1   MSNDVFDGQLLAEKLSKLNNSQQSIESLSRWCISHRKKAKQIVETWDKLFNSSQKEQCVS 60

Query: 61  FLYLANDILQNSRRKGSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFG 120
           FLYLANDILQNSRRKGSEFVNEFWKVLP ALKHVYDNGDEYGKKAV+RLVDIWEERKVFG
Sbjct: 61  FLYLANDILQNSRRKGSEFVNEFWKVLPLALKHVYDNGDEYGKKAVSRLVDIWEERKVFG 120

Query: 121 SRGQGLKDEMLGKNPPPVPASNGRSSNPIKIVKRDANSVRIKLAVGALPEKILTAFQSVL 180
           SRGQGLKDEMLGK+ PP+  SNG++SNPIKIVKRD+ SVRIKL++G +PEKI+TAFQ+V 
Sbjct: 121 SRGQGLKDEMLGKS-PPLLVSNGKNSNPIKIVKRDSQSVRIKLSIGGMPEKIVTAFQTVH 179

Query: 181 DEHPNEEVALNNCNAAVHHAGKVSEDVENT 210
           DE  NEE  LN C  AV H GK+  D  NT
Sbjct: 180 DEQVNEEAVLNKCKTAVQHVGKLEVDAGNT 209

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296085856|emb|CBI31180.3| unnamed protein product [Vitis vinifera]

 Score =  360 bits (923), Expect = 3e-97,   Method: Compositional matrix adjust.
 Identities = 171/213 (80%), Positives = 188/213 (88%), Gaps = 1/213 (0%)

Query: 1   MSNEAFDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVS 60
           MSN+ FDGQ+L+EKLSKLNNSQQSIESLSRWCI+HRKKAKQIVETWDK FNSSQKEQ VS
Sbjct: 1   MSNDVFDGQLLAEKLSKLNNSQQSIESLSRWCISHRKKAKQIVETWDKLFNSSQKEQCVS 60

Query: 61  FLYLANDILQNSRRKGSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFG 120
           FLYLANDILQNSRRKGSEFVNEFWKVLP ALKHVYDNGDEYGKKAV+RLVDIWEERKVFG
Sbjct: 61  FLYLANDILQNSRRKGSEFVNEFWKVLPLALKHVYDNGDEYGKKAVSRLVDIWEERKVFG 120

Query: 121 SRGQGLKDEMLGKNPPPVPASNGRSSNPIKIVKRDANSVRIKLAVGALPEKILTAFQSVL 180
           SRGQGLKDEMLGK+ PP+  SNG++SNPIKIVKRD+ SVRIKL++G +PEKI+TAFQ+V 
Sbjct: 121 SRGQGLKDEMLGKS-PPLLVSNGKNSNPIKIVKRDSQSVRIKLSIGGMPEKIVTAFQTVH 179

Query: 181 DEHPNEEVALNNCNAAVHHAGKVSEDVENTPSQ 213
           DE  NEE  LN C  AV H GK+  D  NT  +
Sbjct: 180 DEQVNEEAVLNKCKTAVQHVGKLEVDAGNTSGE 212

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356506176|ref|XP_003521863.1| PREDICTED: uncharacterized protein LOC100814308 [Glycine max]

 Score =  358 bits (920), Expect = 6e-97,   Method: Compositional matrix adjust.
 Identities = 173/213 (81%), Positives = 194/213 (91%), Gaps = 1/213 (0%)

Query: 1   MSNEAFDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVS 60
           MSN+ FD Q+L+EKL KLNNSQQSIESLS WCI+HRK+AK+IVETWDK FN+SQKEQRVS
Sbjct: 1   MSNDIFDRQLLAEKLLKLNNSQQSIESLSHWCISHRKRAKEIVETWDKLFNASQKEQRVS 60

Query: 61  FLYLANDILQNSRRKGSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFG 120
           FLYLANDILQNSRRKGSEFVNEFWKVLPAAL+HVY++GDE G+KAVTRLVDIWEERKVFG
Sbjct: 61  FLYLANDILQNSRRKGSEFVNEFWKVLPAALRHVYESGDEDGRKAVTRLVDIWEERKVFG 120

Query: 121 SRGQGLKDEMLGKNPPPVPASNGRSSNPIKIVKRDANSVRIKLAVGALPEKILTAFQSVL 180
           SRGQGLKD+++GKNP P  ASNG+SSN IKIVKRDA+SVRIKLAVG LPEKILTAFQ +L
Sbjct: 121 SRGQGLKDDVMGKNPLPS-ASNGKSSNSIKIVKRDAHSVRIKLAVGGLPEKILTAFQPIL 179

Query: 181 DEHPNEEVALNNCNAAVHHAGKVSEDVENTPSQ 213
           D+H NEE +LNNC+AAV   GKV EDVENT +Q
Sbjct: 180 DQHLNEEASLNNCSAAVREVGKVVEDVENTLAQ 212

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255580264|ref|XP_002530962.1| conserved hypothetical protein [Ricinus communis] gi|223529477|gb|EEF31434.1| conserved hypothetical protein [Ricinus communis]

 Score =  346 bits (887), Expect = 4e-93,   Method: Compositional matrix adjust.
 Identities = 160/209 (76%), Positives = 187/209 (89%)

Query: 1   MSNEAFDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVS 60
           MSN+ FD QIL+EKLSKLNNSQQSIESLSRWCI HRKKA+ IVE WDK FNSSQ+EQRVS
Sbjct: 1   MSNDVFDAQILTEKLSKLNNSQQSIESLSRWCILHRKKARPIVEIWDKLFNSSQREQRVS 60

Query: 61  FLYLANDILQNSRRKGSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFG 120
           FLYLANDILQNS+RKGSEFVNEFWK LPAALK VY+NGDE GKKAVTRLVDIWEERKVFG
Sbjct: 61  FLYLANDILQNSKRKGSEFVNEFWKALPAALKQVYENGDENGKKAVTRLVDIWEERKVFG 120

Query: 121 SRGQGLKDEMLGKNPPPVPASNGRSSNPIKIVKRDANSVRIKLAVGALPEKILTAFQSVL 180
           SRGQGLKDEMLGKNPPP+  SNG+SSN I+++KRDA+S+R +LA+G LPEKI++A+QSV+
Sbjct: 121 SRGQGLKDEMLGKNPPPLLVSNGKSSNLIRLLKRDAHSIRYRLALGGLPEKIVSAYQSVI 180

Query: 181 DEHPNEEVALNNCNAAVHHAGKVSEDVEN 209
           DE  +EE A+N C+ AV + GK+ E++E+
Sbjct: 181 DEVSSEEAAINKCSTAVSNVGKIREEIES 209

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357508995|ref|XP_003624786.1| Regulation of nuclear pre-mRNA domain-containing protein 1B [Medicago truncatula] gi|355499801|gb|AES81004.1| Regulation of nuclear pre-mRNA domain-containing protein 1B [Medicago truncatula]

 Score =  335 bits (859), Expect = 7e-90,   Method: Compositional matrix adjust.
 Identities = 165/225 (73%), Positives = 187/225 (83%), Gaps = 12/225 (5%)

Query: 1   MSNEAFDGQILSEKLSKLNNSQQSIE------------SLSRWCITHRKKAKQIVETWDK 48
           MS++ FDGQ+L+EKL KLNNSQQSIE            +LSRWCI H+K+AK IVE WDK
Sbjct: 19  MSDDIFDGQMLAEKLLKLNNSQQSIECIQSAVEIPRHSALSRWCIPHQKRAKDIVEIWDK 78

Query: 49  SFNSSQKEQRVSFLYLANDILQNSRRKGSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTR 108
            FN+SQKEQRVSFL LANDILQNSRRKGSEFVNEFWKVLPAAL+HVY++GD  G+KAV R
Sbjct: 79  LFNASQKEQRVSFLNLANDILQNSRRKGSEFVNEFWKVLPAALRHVYESGDVQGRKAVNR 138

Query: 109 LVDIWEERKVFGSRGQGLKDEMLGKNPPPVPASNGRSSNPIKIVKRDANSVRIKLAVGAL 168
           L+DIWEERKVFGSR QGLKDE++ KNP P  A+NG+ S+PIKIVKRDA+SVRIKLAVG+L
Sbjct: 139 LIDIWEERKVFGSRSQGLKDEVMSKNPLPFSANNGKGSDPIKIVKRDAHSVRIKLAVGSL 198

Query: 169 PEKILTAFQSVLDEHPNEEVALNNCNAAVHHAGKVSEDVENTPSQ 213
           PEKILTAF SVLDEH NEE ALN CNA VH   K+ EDVENT +Q
Sbjct: 199 PEKILTAFHSVLDEHLNEEAALNKCNAGVHDVVKLLEDVENTFAQ 243

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255635643|gb|ACU18171.1| unknown [Glycine max]

 Score =  311 bits (796), Expect = 1e-82,   Method: Compositional matrix adjust.
 Identities = 151/181 (83%), Positives = 168/181 (92%), Gaps = 1/181 (0%)

Query: 1   MSNEAFDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVS 60
           MSN+ FD Q+L+EKL KLNNSQQSI SLS WCI+HRK+AK+IVETWDK FN+SQKEQRVS
Sbjct: 1   MSNDIFDRQLLAEKLLKLNNSQQSIGSLSHWCISHRKRAKEIVETWDKLFNASQKEQRVS 60

Query: 61  FLYLANDILQNSRRKGSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFG 120
           FLYLANDILQNSRRKGSEFVNEFWKVLPAAL+HVY++GDE G+KAVTRLVDIWEERKVFG
Sbjct: 61  FLYLANDILQNSRRKGSEFVNEFWKVLPAALRHVYESGDEDGRKAVTRLVDIWEERKVFG 120

Query: 121 SRGQGLKDEMLGKNPPPVPASNGRSSNPIKIVKRDANSVRIKLAVGALPEKILTAFQSVL 180
           SRGQGLKD+++GKNP P  ASNG+SSN IKIVKRDA+SVRIKLAVG LPEKILTAFQ +L
Sbjct: 121 SRGQGLKDDVMGKNPLP-SASNGKSSNSIKIVKRDAHSVRIKLAVGGLPEKILTAFQPIL 179

Query: 181 D 181
           D
Sbjct: 180 D 180

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357497311|ref|XP_003618944.1| Regulation of nuclear pre-mRNA domain-containing protein 1B [Medicago truncatula] gi|355493959|gb|AES75162.1| Regulation of nuclear pre-mRNA domain-containing protein 1B [Medicago truncatula]

 Score =  305 bits (780), Expect = 1e-80,   Method: Compositional matrix adjust.
 Identities = 152/213 (71%), Positives = 179/213 (84%), Gaps = 8/213 (3%)

Query: 1   MSNEAFDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVS 60
           M N+A+DGQ+L+EKL KLNNSQQSIES+SR C++HRK+AK IVETW+KSF SSQKEQRV 
Sbjct: 1   MGNDAYDGQVLAEKLRKLNNSQQSIESVSRLCVSHRKRAKDIVETWNKSFGSSQKEQRVP 60

Query: 61  FLYLANDILQNSRRKGSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFG 120
           FL LANDILQNSRRKGSEFVNEFWKVLP+ALK VY + DE GKK+V RL+DIWEERKVFG
Sbjct: 61  FLNLANDILQNSRRKGSEFVNEFWKVLPSALKRVYAS-DEPGKKSVIRLIDIWEERKVFG 119

Query: 121 SRGQGLKDEMLGKNPPPVPASNGRSSNPIKIVKRDANSVRIKLAVGALPEKILTAFQSVL 180
           SR QGLK+E+ GK       SNG++SNPIKI KRDA+S+R+KLA+G LPEKI+TA   V 
Sbjct: 120 SRSQGLKEEITGK-------SNGKNSNPIKIAKRDAHSLRLKLAIGCLPEKIITALHFVN 172

Query: 181 DEHPNEEVALNNCNAAVHHAGKVSEDVENTPSQ 213
           +EHPNEE +LN C+AA+   GK+ EDVENT SQ
Sbjct: 173 EEHPNEEASLNKCSAALSQLGKLVEDVENTLSQ 205

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356514068|ref|XP_003525729.1| PREDICTED: uncharacterized protein LOC100791478 [Glycine max]

 Score =  300 bits (768), Expect = 3e-79,   Method: Compositional matrix adjust.
 Identities = 142/187 (75%), Positives = 163/187 (87%), Gaps = 1/187 (0%)

Query: 27  SLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRKGSEFVNEFWKV 86
           +LSR CI+HRK+AK+IVETWDK F+SSQKEQ +SFLYLANDILQNS+RKG EFVNEFWKV
Sbjct: 23  ALSRLCISHRKRAKEIVETWDKLFSSSQKEQCISFLYLANDILQNSKRKGGEFVNEFWKV 82

Query: 87  LPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGSRGQGLKDEMLGKNPPPVPASNGRSS 146
           LPAAL+ VYD+ DE+GKKAVTRL+DIWEERKVFGSRGQGLKDE++G+NP P   SNG+SS
Sbjct: 83  LPAALRRVYDS-DEHGKKAVTRLIDIWEERKVFGSRGQGLKDEIMGQNPLPSSTSNGKSS 141

Query: 147 NPIKIVKRDANSVRIKLAVGALPEKILTAFQSVLDEHPNEEVALNNCNAAVHHAGKVSED 206
           NPIKIVKRDA+SVR+KLAVG LPEK+LT+  SV DEH NEE ALN CNA VH  GK+ ED
Sbjct: 142 NPIKIVKRDAHSVRLKLAVGCLPEKLLTSLHSVHDEHLNEEFALNKCNAVVHQVGKLVED 201

Query: 207 VENTPSQ 213
            EN  +Q
Sbjct: 202 AENILAQ 208

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147828708|emb|CAN66227.1| hypothetical protein VITISV_012976 [Vitis vinifera]

 Score =  295 bits (756), Expect = 7e-78,   Method: Compositional matrix adjust.
 Identities = 148/220 (67%), Positives = 165/220 (75%), Gaps = 31/220 (14%)

Query: 22  QQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRKGSEFVN 81
           ++ + +LSRWCI+HRKKAKQIVETWDK FNSSQKEQ VSFLYLANDILQNSRRKGSEFVN
Sbjct: 576 EEVVTTLSRWCISHRKKAKQIVETWDKLFNSSQKEQCVSFLYLANDILQNSRRKGSEFVN 635

Query: 82  EFWKVLPAALKHVYDNGDEYGKKAVTRL----------------------------VDIW 113
           EFWKVLP ALKHVYDNGDEYGKKAV+RL                            VDIW
Sbjct: 636 EFWKVLPLALKHVYDNGDEYGKKAVSRLVPXIDWVPPKRVKDMLIMSFKGIGGFLEVDIW 695

Query: 114 EERKVFGSRGQGLKDEMLGKNPPPVPASNGRSSNPIKIVKRDANSVRIKLAVGALPEKIL 173
           EERKVFGSRGQGLKDEMLGK+PPP+  SNG++SNPIKIVKRD+ S   KL+VG +PEKI+
Sbjct: 696 EERKVFGSRGQGLKDEMLGKSPPPLLVSNGKNSNPIKIVKRDSQS---KLSVGGMPEKIV 752

Query: 174 TAFQSVLDEHPNEEVALNNCNAAVHHAGKVSEDVENTPSQ 213
           TAFQ+V DE  NEE ALN C  AV H GK+  D  NT  +
Sbjct: 753 TAFQTVHDEQVNEEAALNKCKTAVQHVGKLEVDAGNTSGE 792

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	213
TAIR|locus:2171795	439	AT5G65180 "AT5G65180" [Arabido	0.967	0.469	0.528	2.6e-54
TAIR|locus:2184113	469	AT5G10060 "AT5G10060" [Arabido	0.981	0.445	0.523	1.3e-52
TAIR|locus:2091990	513	AT3G26990 "AT3G26990" [Arabido	0.906	0.376	0.507	1.8e-48
MGI|MGI:1917720	326	Rprd1b "regulation of nuclear	0.661	0.432	0.461	2.4e-28
RGD|1304782	224	Rprd1b "regulation of nuclear	0.661	0.629	0.461	2.4e-28
UNIPROTKB|A6QLW3	326	RPRD1B "RPRD1B protein" [Bos t	0.661	0.432	0.454	6.4e-28
UNIPROTKB|E2RRZ8	326	RPRD1B "Uncharacterized protei	0.661	0.432	0.454	6.4e-28
UNIPROTKB|Q9NQG5	326	RPRD1B "Regulation of nuclear	0.661	0.432	0.454	6.4e-28
UNIPROTKB|F2Z5H3	326	RPRD1B "Uncharacterized protei	0.661	0.432	0.454	6.4e-28
UNIPROTKB|Q5F4B4	325	CREPT "Cell-cycle related and	0.619	0.406	0.473	1.7e-27

TAIR|locus:2171795 AT5G65180 "AT5G65180" [Arabidopsis thaliana (taxid:3702)]

 Score = 561 (202.5 bits), Expect = 2.6e-54, P = 2.6e-54
 Identities = 110/208 (52%), Positives = 148/208 (71%)

Query:     6 FDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLA 65
             F  +IL + L+KLN++QQSI++LS+WCI HR +A+ +V TW+K F+S+Q  Q+V  LYLA
Sbjct:     5 FSEEILIDNLAKLNSTQQSIQTLSQWCIVHRSEAELVVTTWEKQFHSTQIGQKVPLLYLA 64

Query:    66 NDILQNSRRKGSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGSRGQG 125
             NDILQNS+R+G+EFV EFWKVLP ALK +   GD+YGK  V+RLV+IWEER+VFGSR + 
Sbjct:    65 NDILQNSKRQGNEFVQEFWKVLPGALKDIVSLGDDYGKGVVSRLVNIWEERRVFGSRSKS 124

Query:   126 LKDEMLGKN-PPPVPASNGRSSNPIKIVKRDANSVRIKLAVGALPEKILTAFQSVLDEHP 184
             LKD ML +  PPP+  S  R     K  KRD+ S + KL+ G + EKI++AF  V  E+ 
Sbjct:   125 LKDVMLSEEAPPPLDVSKKRFRGS-KSAKRDSKSTKTKLSSGGVSEKIVSAFNLVRAENS 183

Query:   185 NEEVALNNCNAAVHHAGKVSEDVENTPS 212
             NEE  +N C +AV    K+ +DVE+  S
Sbjct:   184 NEETEMNKCKSAVRRIRKMEKDVEDACS 211

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0007059 "chromosome segregation" evidence=RCA

GO:0007062 "sister chromatid cohesion" evidence=RCA

GO:0007129 "synapsis" evidence=RCA

GO:0007131 "reciprocal meiotic recombination" evidence=RCA

GO:0010332 "response to gamma radiation" evidence=RCA

GO:0031048 "chromatin silencing by small RNA" evidence=RCA

GO:0032204 "regulation of telomere maintenance" evidence=RCA

GO:0032504 "multicellular organism reproduction" evidence=RCA

GO:0033044 "regulation of chromosome organization" evidence=RCA

GO:0042138 "meiotic DNA double-strand break formation" evidence=RCA

GO:0043247 "telomere maintenance in response to DNA damage" evidence=RCA

GO:0045132 "meiotic chromosome segregation" evidence=RCA

TAIR|locus:2184113 AT5G10060 "AT5G10060" [Arabidopsis thaliana (taxid:3702)]

 Score = 545 (196.9 bits), Expect = 1.3e-52, P = 1.3e-52
 Identities = 111/212 (52%), Positives = 147/212 (69%)

Query:     3 NEAFDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFL 62
             +  F  QIL +KL+KLN+SQQSIE+LS WCI +R KA+ IV TW+K F+S++ +Q+V  L
Sbjct:     2 SSVFSDQILIDKLAKLNSSQQSIETLSHWCIFNRSKAELIVTTWEKQFHSTEMDQKVPLL 61

Query:    63 YLANDILQNSRRKGSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGSR 122
             YLANDILQNS+R+G+EFV EFW VLP ALK +   GD+ GK AV R++ IWEER+VFGSR
Sbjct:    62 YLANDILQNSKRQGNEFVQEFWNVLPKALKDIVSQGDDNGKSAVARVIKIWEERRVFGSR 121

Query:   123 GQGLKDEMLGKNPP-PVPASNGRSSNPIKIVKRDANSVRIKLAV-GALPEKILTAFQSVL 180
              + LKD MLG++ P P+  S  R     K  KR++ S R KLA  G + EKI +A+  V+
Sbjct:   122 SKSLKDVMLGEDVPLPLDISKKRPRGS-KSSKRESKSSRTKLASSGGVAEKIASAYHLVV 180

Query:   181 DEHPNEEVALNNCNAAVHHAGKVSEDVENTPS 212
              E+ NEE  +N C +AV    K+ +DVE   S
Sbjct:   181 AENSNEEAEMNKCKSAVKRIRKMEKDVEEACS 212

GO:0003674 "molecular_function" evidence=ND

GO:0005576 "extracellular region" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2091990 AT3G26990 "AT3G26990" [Arabidopsis thaliana (taxid:3702)]

 Score = 506 (183.2 bits), Expect = 1.8e-48, P = 1.8e-48
 Identities = 105/207 (50%), Positives = 145/207 (70%)

Query:     5 AFDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYL 64
             +F+ QIL EKL+KLNNSQ SIE+LS WCI H  KAK +VETW + F+ + +EQR+++LYL
Sbjct:     4 SFNAQILVEKLAKLNNSQASIETLSHWCIFHMNKAKHVVETWGRQFHCAPREQRLAYLYL 63

Query:    65 ANDILQNSRRKGSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGSRGQ 124
             ANDILQNSRRKGSEFV EFWKVLP AL+ + +NGD++G+K+  RLV+IWEERKVFGSRGQ
Sbjct:    64 ANDILQNSRRKGSEFVGEFWKVLPDALRDMIENGDDFGRKSARRLVNIWEERKVFGSRGQ 123

Query:   125 GLKDEMLGKNPPPVPASNG-RSSN--PIKIVKRDANSVRIKLAVGALPEKILTAFQSVLD 181
              LK+E+LG+ P      NG R+ N  P+K+      SV  +   G+  EK+++A + +  
Sbjct:   124 ILKEELLGRQP-----ENGTRNGNLVPLKL------SVPQRQVNGSTLEKVVSAVEVLHG 172

Query:   182 EHPNEEVALNNCNAAVHHAGKVSEDVE 208
                +E+  +     A  +  K +++VE
Sbjct:   173 VQIDEDALVGKSTNAAGYLEKATQEVE 199

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

MGI|MGI:1917720 Rprd1b "regulation of nuclear pre-mRNA domain containing 1B" [Mus musculus (taxid:10090)]

 Score = 316 (116.3 bits), Expect = 2.4e-28, P = 2.4e-28
 Identities = 66/143 (46%), Positives = 90/143 (62%)

Query:     5 AFDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYL 64
             +F    L +KLS+L+NSQQS+++LS W I HRK A  IV  W +    ++  ++++FLYL
Sbjct:     3 SFSESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLYL 62

Query:    65 ANDILQNSRRKGSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGSRG- 123
             AND++QNS+RKG EF  EF  VL  A  HV    DE  KK + RL++IW+ER V+G    
Sbjct:    63 ANDVIQNSKRKGPEFTREFESVLVDAFSHVAREADEGCKKPLERLLNIWQERSVYGGEFI 122

Query:   124 QGLKDEML-GKNPPPVPASNGRS 145
             Q LK  M   K+PPP  A   +S
Sbjct:   123 QQLKLSMEDSKSPPPKAAEEKKS 145

GO:0000993 "RNA polymerase II core binding" evidence=ISO

GO:0005634 "nucleus" evidence=ISO

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0008284 "positive regulation of cell proliferation" evidence=ISO

GO:0010564 "regulation of cell cycle process" evidence=ISO

GO:0016591 "DNA-directed RNA polymerase II, holoenzyme" evidence=ISO

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=ISO

GO:0070940 "dephosphorylation of RNA polymerase II C-terminal domain" evidence=ISO

RGD|1304782 Rprd1b "regulation of nuclear pre-mRNA domain containing 1B" [Rattus norvegicus (taxid:10116)]

 Score = 316 (116.3 bits), Expect = 2.4e-28, P = 2.4e-28
 Identities = 66/143 (46%), Positives = 90/143 (62%)

Query:     5 AFDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYL 64
             +F    L +KLS+L+NSQQS+++LS W I HRK A  IV  W +    ++  ++++FLYL
Sbjct:     3 SFSESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLYL 62

Query:    65 ANDILQNSRRKGSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGSRG- 123
             AND++QNS+RKG EF  EF  VL  A  HV    DE  KK + RL++IW+ER V+G    
Sbjct:    63 ANDVIQNSKRKGPEFTREFESVLVDAFSHVAREADEGCKKPLERLLNIWQERSVYGGEFI 122

Query:   124 QGLKDEML-GKNPPPVPASNGRS 145
             Q LK  M   K+PPP  A   +S
Sbjct:   123 QQLKLSMEDSKSPPPKAAEEKKS 145

GO:0000993 "RNA polymerase II core binding" evidence=ISO

GO:0005634 "nucleus" evidence=ISO

GO:0008284 "positive regulation of cell proliferation" evidence=ISO

GO:0010564 "regulation of cell cycle process" evidence=ISO

GO:0016591 "DNA-directed RNA polymerase II, holoenzyme" evidence=ISO

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=ISO

GO:0070940 "dephosphorylation of RNA polymerase II C-terminal domain" evidence=ISO

UNIPROTKB|A6QLW3 RPRD1B "RPRD1B protein" [Bos taurus (taxid:9913)]

 Score = 312 (114.9 bits), Expect = 6.4e-28, P = 6.4e-28
 Identities = 65/143 (45%), Positives = 89/143 (62%)

Query:     5 AFDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYL 64
             +F    L +KLS+L+NSQQS+++LS W I HRK A  IV  W +    ++  ++++FLYL
Sbjct:     3 SFSESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLYL 62

Query:    65 ANDILQNSRRKGSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGSRG- 123
             AND++QNS+RKG EF  EF  VL  A  HV    DE  KK + RL++IW+ER V+G    
Sbjct:    63 ANDVIQNSKRKGPEFTREFESVLVDAFSHVAREADEGCKKPLERLLNIWQERSVYGGEFI 122

Query:   124 QGLKDEML-GKNPPPVPASNGRS 145
             Q LK  M   K+PPP      +S
Sbjct:   123 QQLKLSMEDSKSPPPKATEEKKS 145

GO:0070940 "dephosphorylation of RNA polymerase II C-terminal domain" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0016591 "DNA-directed RNA polymerase II, holoenzyme" evidence=IEA

GO:0010564 "regulation of cell cycle process" evidence=IEA

GO:0008284 "positive regulation of cell proliferation" evidence=IEA

GO:0000993 "RNA polymerase II core binding" evidence=IEA

UNIPROTKB|E2RRZ8 RPRD1B "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 312 (114.9 bits), Expect = 6.4e-28, P = 6.4e-28
 Identities = 65/143 (45%), Positives = 89/143 (62%)

Query:     5 AFDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYL 64
             +F    L +KLS+L+NSQQS+++LS W I HRK A  IV  W +    ++  ++++FLYL
Sbjct:     3 SFSESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLYL 62

Query:    65 ANDILQNSRRKGSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGSRG- 123
             AND++QNS+RKG EF  EF  VL  A  HV    DE  KK + RL++IW+ER V+G    
Sbjct:    63 ANDVIQNSKRKGPEFTREFESVLVDAFSHVAREADEGCKKPLERLLNIWQERSVYGGEFI 122

Query:   124 QGLKDEML-GKNPPPVPASNGRS 145
             Q LK  M   K+PPP      +S
Sbjct:   123 QQLKLSMEDSKSPPPKATEEKKS 145

GO:0070940 "dephosphorylation of RNA polymerase II C-terminal domain" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0016591 "DNA-directed RNA polymerase II, holoenzyme" evidence=IEA

GO:0010564 "regulation of cell cycle process" evidence=IEA

GO:0008284 "positive regulation of cell proliferation" evidence=IEA

GO:0000993 "RNA polymerase II core binding" evidence=IEA

UNIPROTKB|Q9NQG5 RPRD1B "Regulation of nuclear pre-mRNA domain-containing protein 1B" [Homo sapiens (taxid:9606)]

 Score = 312 (114.9 bits), Expect = 6.4e-28, P = 6.4e-28
 Identities = 65/143 (45%), Positives = 89/143 (62%)

Query:     5 AFDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYL 64
             +F    L +KLS+L+NSQQS+++LS W I HRK A  IV  W +    ++  ++++FLYL
Sbjct:     3 SFSESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLYL 62

Query:    65 ANDILQNSRRKGSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGSRG- 123
             AND++QNS+RKG EF  EF  VL  A  HV    DE  KK + RL++IW+ER V+G    
Sbjct:    63 ANDVIQNSKRKGPEFTREFESVLVDAFSHVAREADEGCKKPLERLLNIWQERSVYGGEFI 122

Query:   124 QGLKDEML-GKNPPPVPASNGRS 145
             Q LK  M   K+PPP      +S
Sbjct:   123 QQLKLSMEDSKSPPPKATEEKKS 145

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0016591 "DNA-directed RNA polymerase II, holoenzyme" evidence=IDA

GO:0070940 "dephosphorylation of RNA polymerase II C-terminal domain" evidence=IMP

GO:0005634 "nucleus" evidence=IDA

GO:0008284 "positive regulation of cell proliferation" evidence=IDA

GO:0010564 "regulation of cell cycle process" evidence=IDA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IDA

GO:0000993 "RNA polymerase II core binding" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

UNIPROTKB|F2Z5H3 RPRD1B "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 312 (114.9 bits), Expect = 6.4e-28, P = 6.4e-28
 Identities = 65/143 (45%), Positives = 89/143 (62%)

Query:     5 AFDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYL 64
             +F    L +KLS+L+NSQQS+++LS W I HRK A  IV  W +    ++  ++++FLYL
Sbjct:     3 SFSESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLYL 62

Query:    65 ANDILQNSRRKGSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGSRG- 123
             AND++QNS+RKG EF  EF  VL  A  HV    DE  KK + RL++IW+ER V+G    
Sbjct:    63 ANDVIQNSKRKGPEFTREFESVLVDAFSHVAREADEGCKKPLERLLNIWQERSVYGGEFI 122

Query:   124 QGLKDEML-GKNPPPVPASNGRS 145
             Q LK  M   K+PPP      +S
Sbjct:   123 QQLKLSMEDSKSPPPKATEEKKS 145

GO:0070940 "dephosphorylation of RNA polymerase II C-terminal domain" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0016591 "DNA-directed RNA polymerase II, holoenzyme" evidence=IEA

GO:0010564 "regulation of cell cycle process" evidence=IEA

GO:0008284 "positive regulation of cell proliferation" evidence=IEA

GO:0000993 "RNA polymerase II core binding" evidence=IEA

UNIPROTKB|Q5F4B4 CREPT "Cell-cycle related and expression-elevated protein in tumor" [Gallus gallus (taxid:9031)]

 Score = 308 (113.5 bits), Expect = 1.7e-27, P = 1.7e-27
 Identities = 63/133 (47%), Positives = 85/133 (63%)

Query:     5 AFDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYL 64
             +F    L +KLS+L+NSQQS+++LS W I HRK A  IV  W +    ++  ++++FLYL
Sbjct:     3 SFSESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSSRKLTFLYL 62

Query:    65 ANDILQNSRRKGSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGSRG- 123
             AND++QNS+RKG EF  EF  VL  A  HV    DE  KK + RL++IW+ER V+GS   
Sbjct:    63 ANDVIQNSKRKGPEFTREFESVLVDAFSHVAREADEGCKKPLERLLNIWQERSVYGSEFI 122

Query:   124 QGLKDEMLGKNPP 136
             Q LK  M   N P
Sbjct:   123 QQLKLSMEDSNSP 135

GO:0000993 "RNA polymerase II core binding" evidence=IEA

GO:0008284 "positive regulation of cell proliferation" evidence=IEA

GO:0010564 "regulation of cell cycle process" evidence=IEA

GO:0016591 "DNA-directed RNA polymerase II, holoenzyme" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0070940 "dephosphorylation of RNA polymerase II C-terminal domain" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00033676001 SubName- Full=Chromosome chr8 scaffold_68, whole genome shotgun sequence; (593 aa) (Vitis vinifera)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	213
smart00582	124	smart00582, RPR, domain present in proteins, which	2e-39
cd03562	114	cd03562, CID, CID (CTD-Interacting Domain) domain	1e-36
pfam04818	64	pfam04818, CTD_bind, RNA polymerase II-binding dom	4e-24

>gnl|CDD|214731 smart00582, RPR, domain present in proteins, which are involved in regulation of nuclear pre-mRNA

 Score =  131 bits (331), Expect = 2e-39
 Identities = 49/111 (44%), Positives = 70/111 (63%), Gaps = 1/111 (0%)

Query: 11  LSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQ 70
             +KL  LNNSQ+SI++L++W I H   AK+IVE W+K    +   +++  LYL + I+Q
Sbjct: 2   FEQKLESLNNSQESIQTLTKWAIEHASHAKEIVELWEKYIKKAPVPRKLPLLYLLDSIVQ 61

Query: 71  NSRRK-GSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFG 120
           NS+RK GSEF +E   V   AL+ V     E  KK + RL++IWEER +F 
Sbjct: 62  NSKRKYGSEFGDELGPVFQDALRRVLGAAPEELKKKIRRLLNIWEERGIFP 112

Length = 124

>gnl|CDD|239621 cd03562, CID, CID (CTD-Interacting Domain) domain family; CID is present in several RNA-processing factors such as Pcf11 and Nrd1

 Score =  123 bits (312), Expect = 1e-36
 Identities = 50/117 (42%), Positives = 69/117 (58%), Gaps = 3/117 (2%)

Query: 5   AFDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYL 64
            FD   L EKL+   NSQ SI++L++  I +RK AK+IVE  +K       EQ++  LYL
Sbjct: 1   VFDYNALLEKLTFNKNSQPSIQTLTKLAIENRKHAKEIVEIIEKHIKKCPPEQKLPLLYL 60

Query: 65  ANDILQNSRRKGSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGS 121
            + I++N  RK  EF +EF   L       Y+  DE  +K + RL++IWEER VFGS
Sbjct: 61  LDSIVKNVGRKYKEFFSEF---LVPLFLDAYEKVDEKTRKKLERLLNIWEERFVFGS 114

Pcf11 is a conserved and essential subunit of the yeast cleavage factor IA, which is required for polyadenylation-dependent 3'-RNA processing and transcription termination. Nrd1 is implicated in polyadenylation-independent 3'-RNA processing. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II. During transcription, Pol II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr 1-Ser 2-Pro 3-Thr 4-Ser 5-Pro 6-Ser 7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices. Length = 114

>gnl|CDD|218279 pfam04818, CTD_bind, RNA polymerase II-binding domain

 Score = 90.4 bits (225), Expect = 4e-24
 Identities = 35/64 (54%), Positives = 43/64 (67%), Gaps = 1/64 (1%)

Query: 58  RVSFLYLANDILQNSRRKG-SEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEER 116
           ++  LYLAND++QNS+ K   EFV  F  VLP A  HVY  GDE  KK + RL++IWEER
Sbjct: 1   KLPLLYLANDVVQNSKHKNKDEFVKAFSPVLPDAFAHVYKEGDEEVKKKIRRLLNIWEER 60

Query: 117 KVFG 120
            VF 
Sbjct: 61  NVFS 64

This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase II. Length = 64

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	213
KOG2669	325	consensus Regulator of nuclear mRNA [RNA processin	100.0
smart00582	121	RPR domain present in proteins, which are involved	99.96
cd03562	114	CID CID (CTD-Interacting Domain) domain family; CI	99.94
PF04818	64	CTD_bind: RNA polymerase II-binding domain.; Inter	99.83
KOG0151	877	consensus Predicted splicing regulator, contains R	99.73
PF12243	139	CTK3: CTD kinase subunit gamma CTK3	99.68
KOG4368	757	consensus Predicted RNA binding protein, contains	99.5
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.64
KOG2071	579	consensus mRNA cleavage and polyadenylation factor	98.11
cd00197	115	VHS_ENTH_ANTH VHS, ENTH and ANTH domain superfamil	96.66
PF00790	140	VHS: VHS domain; InterPro: IPR002014 The VHS domai	95.36
cd03561	133	VHS VHS domain family; The VHS domain is present i	94.51
smart00288	133	VHS Domain present in VPS-27, Hrs and STAM. Unpubl	93.77
cd03569	142	VHS_Hrs_Vps27p VHS domain family, Hrs and Vps27p s	93.35
cd03568	144	VHS_STAM VHS domain family, STAM subfamily; member	91.81
cd03567	139	VHS_GGA VHS domain family, GGA subfamily; GGA (Gol	91.17
KOG1087	470	consensus Cytosolic sorting protein GGA2/TOM1 [Int	82.89

>KOG2669 consensus Regulator of nuclear mRNA [RNA processing and modification]

Probab=100.00  E-value=2.6e-42  Score=306.57  Aligned_cols=205  Identities=36%  Similarity=0.590  Sum_probs=177.9

Q ss_pred             CCCCHHHHHHHHhhccCcHHHHHHHHHHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhcChhHHHHH
Q 046621            4 EAFDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRKGSEFVNEF   83 (213)
Q Consensus         4 ~~F~~~~~~~kL~~L~~Sq~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk~~~f~~~F   83 (213)
                      .+|+++.|..||++|++||+|||++|.|||+|+++|+.||++|+++|++++.++||.||||||||+|||+|++++|+++|
T Consensus         2 ~~fsee~l~~kL~~L~~TQeSIqtlS~Wli~hkk~a~~IV~~Wl~~~~~~~~~~Kl~llYLaNDVvQnskrk~~ef~~ef   81 (325)
T KOG2669|consen    2 SAFSEEALEKKLAELSNTQESIQTLSLWLIHHKKHARLIVDVWLKELKKSSVNHKLTLLYLANDVVQNSKRKGPEFVDEF   81 (325)
T ss_pred             CcccHHHHHHHHHhccchHHHHHHHHHHHHHHhhhhhHHHHHHHHHHhccCCCceeeehhhhHHHHHHhhhcCchhHHHH
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhcCChHHHHhHHHHHHHhhhCcccCCCccchhhhhhCCC-CCCCCCCCCCCCCcccccccccchhhhh
Q 046621           84 WKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGSRGQGLKDEMLGKN-PPPVPASNGRSSNPIKIVKRDANSVRIK  162 (213)
Q Consensus        84 ~~vLp~~~~~v~~~~d~~~~~kv~rll~IWeeR~Vf~~~~~~L~~~~lg~~-p~~~~~~~~~~~~~~k~~~~~~~s~~~~  162 (213)
                      +++++.+|.+++..++..++.++.|||+||++|+||+++......++++.. |||.....+ ..+..+..+++.....+.
T Consensus        82 ~~v~~~a~~~i~~~~~~~~k~~l~Rl~nIw~eR~Vf~~~~~~~l~~~l~~e~p~~~d~~~~-~~~~~~~~k~~~~~~~~~  160 (325)
T KOG2669|consen   82 WPVVLKAFAHIVEETDVKCKKKLGRLINIWEERNVFSPESLVDLEESLGAEKPPPLDEAKK-LPRGSKQIKLDEKGSKPG  160 (325)
T ss_pred             HHHHHHHHHHHHHhcchhhhHHHHHHHHHHHHhccCCHHHHHHHHHHhcccCCcchhhhhc-cccchHhhhhhhhccCCC
Confidence            999999999999998888899999999999999999999866666777644 444333332 223445666665554444


Q ss_pred             -cccCCChHHHHHHHHHHHhhCCChHHHHHHhHHHHHHHhhhhhhhhc
Q 046621          163 -LAVGALPEKILTAFQSVLDEHPNEEVALNNCNAAVHHAGKVSEDVEN  209 (213)
Q Consensus       163 -~~~~~~~eki~~~~~~~~~~~~~e~~~~~k~~~~~~~~~~~~~~~~~  209 (213)
                       ...|+++++|.+.++.+-+....+++.+..|+.+..++++|.+++..
T Consensus       161 ~~~~~~v~~~~~~~~~l~~a~~s~~~~~~k~~~~~~~~i~~~~~e~~e  208 (325)
T KOG2669|consen  161 LSSLGEVHEKIDSSVELVRALQSLENAASKLDAVLEERIARLPQEVEE  208 (325)
T ss_pred             CCCccccchhHHhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHH
Confidence             45689999999999888888888999999999999999999888763

>smart00582 RPR domain present in proteins, which are involved in regulation of nuclear pre-mRNA

Probab=99.96  E-value=2e-29  Score=195.46  Aligned_cols=118  Identities=42%  Similarity=0.734  Sum_probs=111.6

Q ss_pred             HHHHHHhhccCcHHHHHHHHHHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhc-ChhHHHHHHHHHH
Q 046621           10 ILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRK-GSEFVNEFWKVLP   88 (213)
Q Consensus        10 ~~~~kL~~L~~Sq~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk-~~~f~~~F~~vLp   88 (213)
                      .|.++|++|++|+++|++++.||++|.+++..||++|.+++.++++++||++|||+|||+|||+++ ++.|..+|.++++
T Consensus         1 ~f~~~L~~L~~s~~~I~~lt~~~~~~~~~a~~Iv~~i~~~~~~~~~~~kL~~LYlindIl~n~~~~~~~~f~~~~~~~~~   80 (121)
T smart00582        1 AFEQKLESLNNSQESIQTLTKWAIEHASHAKEIVELWEKYIKKAPPPRKLPLLYLLDSIVQNSKRKYGSEFGDELGPVFQ   80 (121)
T ss_pred             ChHHHHHhccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccceehhHHhHHHHHHHHhhccHHHHHHHHHHHHH
Confidence            488999999999999999999999999999999999999999999999999999999999999988 5789999999999


Q ss_pred             HHHHHHhhcCChHHHHhHHHHHHHhhhCcccCCCc-cchh
Q 046621           89 AALKHVYDNGDEYGKKAVTRLVDIWEERKVFGSRG-QGLK  127 (213)
Q Consensus        89 ~~~~~v~~~~d~~~~~kv~rll~IWeeR~Vf~~~~-~~L~  127 (213)
                      .++.+++..+++..++++.+||+||++|+||++++ .+|+
T Consensus        81 ~~~~~~~~~~~~~~~~ki~kll~iW~~~~iF~~~~i~~L~  120 (121)
T smart00582       81 DALRDVLGAANDETKKKIRRLLNIWEERGIFPPSVLRPLR  120 (121)
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHHHHhcCCCCCHHHHHHhh
Confidence            99999998878899999999999999999999986 5554

>cd03562 CID CID (CTD-Interacting Domain) domain family; CID is present in several RNA-processing factors such as Pcf11 and Nrd1

Probab=99.94  E-value=1.7e-26  Score=177.71  Aligned_cols=114  Identities=43%  Similarity=0.640  Sum_probs=104.6

Q ss_pred             CCCHHHHHHHHhhccCcHHHHHHHHHHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhcChhHHHHHH
Q 046621            5 AFDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRKGSEFVNEFW   84 (213)
Q Consensus         5 ~F~~~~~~~kL~~L~~Sq~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk~~~f~~~F~   84 (213)
                      .|+.+.+.++|..+++|+++|++++.||++|.++++.||++|.+++.++++.+||++|||+|||+||+++++..+   |.
T Consensus         1 ~~~~~~~l~~L~~~~~S~~~I~~lt~~a~~~~~~a~~iv~~i~~~i~~~~~~~KL~~LYL~dsIvkn~~~~~~~~---~~   77 (114)
T cd03562           1 VFDYNALLEKLTFNKNSQPSIQTLTKLAIENRKHAKEIVEIIEKHIKKCPPEQKLPLLYLLDSIVKNVGRKYKEF---FS   77 (114)
T ss_pred             CccHHHHHHHHHcCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccchHHHHHHHHHHHHcccchHHH---HH
Confidence            367788899999999999999999999999999999999999999999999999999999999999999886543   55


Q ss_pred             HHHHHHHHHHhhcCChHHHHhHHHHHHHhhhCcccCC
Q 046621           85 KVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGS  121 (213)
Q Consensus        85 ~vLp~~~~~v~~~~d~~~~~kv~rll~IWeeR~Vf~~  121 (213)
                      ..++++|.+++..+|+.+++++.||++||++|++|++
T Consensus        78 ~~~~~~f~~~~~~~~~~~r~kl~rl~~iW~~~~~f~~  114 (114)
T cd03562          78 EFLVPLFLDAYEKVDEKTRKKLERLLNIWEERFVFGS  114 (114)
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHHHccCCCCCCC
Confidence            5568899999988999999999999999999999984

Pcf11 is a conserved and essential subunit of the yeast cleavage factor IA, which is required for polyadenylation-dependent 3'-RNA processing and transcription termination. Nrd1 is implicated in polyadenylation-independent 3'-RNA processing. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II. During transcription, Pol II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr 1-Ser 2-Pro 3-Thr 4-Ser 5-Pro 6-Ser 7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.

>PF04818 CTD_bind: RNA polymerase II-binding domain

Probab=99.83  E-value=8.3e-21  Score=132.53  Aligned_cols=63  Identities=54%  Similarity=0.899  Sum_probs=59.1

Q ss_pred             hhHHHHHhHHHHHHhhhcCh-hHHHHHHHHHHHHHHHHhhcCChHHHHhHHHHHHHhhhCcccC
Q 046621           58 RVSFLYLANDILQNSRRKGS-EFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFG  120 (213)
Q Consensus        58 KL~lLYLaNDIlqnskrk~~-~f~~~F~~vLp~~~~~v~~~~d~~~~~kv~rll~IWeeR~Vf~  120 (213)
                      ||++|||+|||+|||++++. +|.++|+++||++|.+++..++++.++++.||++||++|+||+
T Consensus         1 KL~~lYl~ndI~q~sk~k~~~~f~~~F~~~l~~~~~~~~~~~~~~~~~kv~rll~iW~~r~if~   64 (64)
T PF04818_consen    1 KLALLYLANDILQNSKRKNPDEFAPAFSPVLPDAFAHAYKNVDPEVRKKVQRLLNIWEERNIFS   64 (64)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTHCHHHHHHCCHHHHHHHHCCCS-HHHHHHHHHHHHHHHHCTSS-
T ss_pred             CcceeehHHHHHHHhhhcChHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhCCCCCC
Confidence            79999999999999999885 9999999999999999999889999999999999999999996

; InterPro: IPR006903 This entry represents a conserved region found in a number of uncharacterised eukaryotic proteins.; PDB: 2L0I_A 2KM4_A 3D9I_B 3D9N_B 3D9O_A 3D9P_B 3D9K_A 3D9M_A 3D9J_A 3D9L_A ....

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=99.73  E-value=2e-17  Score=158.03  Aligned_cols=129  Identities=25%  Similarity=0.403  Sum_probs=115.6

Q ss_pred             HHHHHHHHhhccCcHHHHHHHHHHHHhchhchHHHHHHHHHHhc--cCcccchhHHHHHhHHHHHHhhhc--C-hhHHHH
Q 046621            8 GQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFN--SSQKEQRVSFLYLANDILQNSRRK--G-SEFVNE   82 (213)
Q Consensus         8 ~~~~~~kL~~L~~Sq~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~--~a~~~~KL~lLYLaNDIlqnskrk--~-~~f~~~   82 (213)
                      ++.|+.+|+.||.-+.+|..++.||+.|...|.+||+|+.+.|.  ..+..+||+.|||+|||||||..+  + +-|+..
T Consensus       433 RdklE~liR~LTpEk~sIg~aM~FalenA~aa~EI~eci~eSlt~~~t~~~kKiarLyLvsDIL~N~sarv~nas~YR~~  512 (877)
T KOG0151|consen  433 RDKLEDLIRGLTPEKSSIGDAMVFALENADAAGEIVECITESLTNKETPLPKKIARLYLVSDILHNSSARVANASAYRKS  512 (877)
T ss_pred             HHHHHHHHHhcCcccchHHHHHHHHHhhhhhHHHHHHHHHHHHhccCCcchhHHHHHHHHHHHHhhhhhhhhHHHHHHHH
Confidence            57899999999999999999999999999999999999999886  467899999999999999999965  3 689999


Q ss_pred             HHHHHHHHHHHHhh---c-----CChHHHHhHHHHHHHhhhCcccCCCc-cchhhhhhCCCCC
Q 046621           83 FWKVLPAALKHVYD---N-----GDEYGKKAVTRLVDIWEERKVFGSRG-QGLKDEMLGKNPP  136 (213)
Q Consensus        83 F~~vLp~~~~~v~~---~-----~d~~~~~kv~rll~IWeeR~Vf~~~~-~~L~~~~lg~~p~  136 (213)
                      |++.|+.+|..++.   .     ..+..+++|++||.+|+++-+|+.++ ..|...++|..+.
T Consensus       513 FEa~L~~Ifd~l~~~yr~I~gRIkaE~fkqRV~kVirvWedW~ifpe~~l~~l~~~Flg~~~~  575 (877)
T KOG0151|consen  513 FEATLEDIFDDLNDLYRSIGGRIKAEAFKQRVMKVIRVWEDWAIFPEDFLIGLQNTFLGLNNI  575 (877)
T ss_pred             HHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHhcCCCC
Confidence            99999999987753   2     24577999999999999999999996 8899999996543

>PF12243 CTK3: CTD kinase subunit gamma CTK3

Probab=99.68  E-value=6e-16  Score=123.90  Aligned_cols=126  Identities=17%  Similarity=0.385  Sum_probs=113.8

Q ss_pred             CCCC-HHHHHHHHhhccCcHHHHHHHHHHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhcC---hhH
Q 046621            4 EAFD-GQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRKG---SEF   79 (213)
Q Consensus         4 ~~F~-~~~~~~kL~~L~~Sq~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk~---~~f   79 (213)
                      |+|. +.+|.+.|++||.|++||+.+.+|++.|+..++.+.+|+++++.+.+.+.|+++||++..+++-|...+   ..|
T Consensus         2 DpFE~r~~F~~~L~~L~aS~qSi~kaa~fAlk~~~~~edL~~cIle~le~~~lN~R~nI~~fID~l~e~~~~~~~~~~~Y   81 (139)
T PF12243_consen    2 DPFEVRMQFTQLLRRLNASQQSIQKAAQFALKNRDMEEDLWSCILEQLEKENLNTRINIFYFIDSLCESSQKSKKYNYPY   81 (139)
T ss_pred             ChHHHHHHHHHHHHHcchhHHHHHHHHHHHHHccccHHHHHHHHHHHHhccchhhHHHHHHHHHHHHHHHHhcccccchh
Confidence            7888 589999999999999999999999999999999999999999999999999999999999999988754   689


Q ss_pred             HHHHHHHHHHHHHHHhhcCCh--HHHHhHHHHHHHhhhCcccCCCc-cchhhh
Q 046621           80 VNEFWKVLPAALKHVYDNGDE--YGKKAVTRLVDIWEERKVFGSRG-QGLKDE  129 (213)
Q Consensus        80 ~~~F~~vLp~~~~~v~~~~d~--~~~~kv~rll~IWeeR~Vf~~~~-~~L~~~  129 (213)
                      +...++.||.++..|.+.+..  .....+.++|+.|.+|++++... .++...
T Consensus        82 v~~l~~dL~~Iv~~V~P~~~~g~~N~~~~~kvL~~~~~k~~l~~~~~~~~~~~  134 (139)
T PF12243_consen   82 VSMLQRDLPRIVDAVAPPDNSGAANLKSVRKVLKNWSKKKILDPEEYEEIEAS  134 (139)
T ss_pred             HHHHHHHHHHHHHHhCCCCCccchHHHHHHHHHHHHHHcCCCCHHHHHHHHHH
Confidence            999999999999999976433  67899999999999999999874 444433

>KOG4368 consensus Predicted RNA binding protein, contains SWAP, RPR and G-patch domains [General function prediction only]

Probab=99.50  E-value=7.3e-14  Score=131.53  Aligned_cols=183  Identities=17%  Similarity=0.310  Sum_probs=135.7

Q ss_pred             CCCHHHHHHHHhhc--cCcHHHHHHHHHHHHhchh---chHHHHHHHHHHhcc--CcccchhHHHHHhHHHHHHhhhcC-
Q 046621            5 AFDGQILSEKLSKL--NNSQQSIESLSRWCITHRK---KAKQIVETWDKSFNS--SQKEQRVSFLYLANDILQNSRRKG-   76 (213)
Q Consensus         5 ~F~~~~~~~kL~~L--~~Sq~SIqs~s~W~l~h~~---~a~~Iv~~w~~~l~~--a~~~~KL~lLYLaNDIlqnskrk~-   76 (213)
                      ..+...|...|+.+  ++|.+.|...+.||+.+++   +++.|+..+...++.  +..+-||+||||+||+++||.||. 
T Consensus       100 ~l~~~~~~~~l~~~~~~c~kd~is~~k~w~f~~~~s~~~~e~~~~~l~n~~~~~~~~~~lrlh~~ylind~~~hcqrk~~  179 (757)
T KOG4368|consen  100 QLDMNEFDNLLQPIIDTCTKDAISAGKNWMFSNAKSPPHCELMAGHLRNRITADGAHFELRLHLIYLINDVLHHCQRKQA  179 (757)
T ss_pred             cCCHHHHHHHHHHHHHHHhHHHHHHhhhhhhhcCCCchHHHHHHHHHHhhhcccccchhhhhhhHHHHHHHHHHHHHHHH
Confidence            45566777777766  5899999999999999988   567888888888875  568899999999999999999986 


Q ss_pred             hhHHHHHHHHHHHHHHHHhhcCChHHHHhHHHHHHHhhhCcccCCCc-cchhhhhhCCCCCCCCCCCCCCCCcccccccc
Q 046621           77 SEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGSRG-QGLKDEMLGKNPPPVPASNGRSSNPIKIVKRD  155 (213)
Q Consensus        77 ~~f~~~F~~vLp~~~~~v~~~~d~~~~~kv~rll~IWeeR~Vf~~~~-~~L~~~~lg~~p~~~~~~~~~~~~~~k~~~~~  155 (213)
                      .+...++++++..+.+..+....+.-.+++.|||..|+.|++|...+ ++|+..++|.....                  
T Consensus       180 ~~~~~~l~~~v~~~yc~~~~~~~e~~~~~~~~ll~~we~~~yf~ds~~~ql~~~~~~~~~~~------------------  241 (757)
T KOG4368|consen  180 RELLAALQKVVVPIYCTSFLAVEEDKQQKIARLLQLWEKNGYFDDSIIQQLQSPALGLGQYQ------------------  241 (757)
T ss_pred             HHHHHHHHHHhHHHHHhhhhhhHhHHHHHHHHHHHHHhhcCchhHHHHHHhhhhhhhhhhHH------------------
Confidence            68999999998888887776666777899999999999999999885 99998887754210                  


Q ss_pred             cchhhhhcccCCChHHHHHHHHHHHhhCCChHHHHHHhHHHHHHHhhhhhhhhcC
Q 046621          156 ANSVRIKLAVGALPEKILTAFQSVLDEHPNEEVALNNCNAAVHHAGKVSEDVENT  210 (213)
Q Consensus       156 ~~s~~~~~~~~~~~eki~~~~~~~~~~~~~e~~~~~k~~~~~~~~~~~~~~~~~~  210 (213)
                         ...+.+-+.+.+-|-.+|+.-++..-.--.  +-...--+-+..||.+|+.+
T Consensus       242 ---~~~~~~y~~~~~~~~~~~~~~~~~~~~qh~--~~~q~~q~q~~~~e~~~~~~  291 (757)
T KOG4368|consen  242 ---ATLINEYSSVVQPVQLAFQQQIQTLKTQHE--EFVQQQQQQMPQMEAEVKAT  291 (757)
T ss_pred             ---HHHHhhhhHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHhhHHHHHhhhcc
Confidence               012233345667777788666553211111  11122334566777777754

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=98.64  E-value=7e-08  Score=94.12  Aligned_cols=125  Identities=23%  Similarity=0.390  Sum_probs=107.9

Q ss_pred             HHHHHHHhhccC-----cHHHHHHHHHHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhc----ChhH
Q 046621            9 QILSEKLSKLNN-----SQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRK----GSEF   79 (213)
Q Consensus         9 ~~~~~kL~~L~~-----Sq~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk----~~~f   79 (213)
                      ..|...|.+|..     |..-|..+....|.|.+.+++||....+++.++..++||.-||+++.|+..++..    ...|
T Consensus         5 ~~Fn~eL~SL~DsK~~IS~sKi~~ITkaAikaIk~ykhVVqsVeKfi~kCkpe~Kl~gLYVIDSIVRqsrhq~~~~kd~F   84 (894)
T KOG0132|consen    5 KEFNGELDSLEDSKPGISGSKILKITKAAIKAIKLYKHVVQSVEKFIKKCKPEYKLPGLYVIDSIVRQSRHQFGKEKDVF   84 (894)
T ss_pred             HHHHHHHHHhhccCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccccCeeEEehHHHHHHHHhhccccccc
Confidence            568888888875     6678999999999999999999999999999999999999999999999999953    2568


Q ss_pred             HHHHHHHHHHHHHHHhhcCChHHHHhHHHHHHHhhhCcccCCCc-cchhhhhhCCC
Q 046621           80 VNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGSRG-QGLKDEMLGKN  134 (213)
Q Consensus        80 ~~~F~~vLp~~~~~v~~~~d~~~~~kv~rll~IWeeR~Vf~~~~-~~L~~~~lg~~  134 (213)
                      ...|..-+-..|..+|.+. .+.+.++.|++++|..++||-.++ +-|.+-..|..
T Consensus        85 ~prf~~n~~~tf~~L~~c~-~edks~iIrvlNlwqkn~VfK~e~IqpLlDm~~~s~  139 (894)
T KOG0132|consen   85 GPRFSKNFTGTFQNLYECP-QEDKSDIIRVLNLWQKNNVFKSEIIQPLLDMADGSG  139 (894)
T ss_pred             CCccchhHHHHHHHHHhcC-HHHHHHHHHhhhhhhcccchhHHHHHHHHHHHhccC
Confidence            8889888999999999874 456888999999999999999996 55666555543

>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]

Probab=98.11  E-value=8.2e-06  Score=78.15  Aligned_cols=103  Identities=23%  Similarity=0.378  Sum_probs=96.4

Q ss_pred             HHHHHHHhhcc-CcHHHHHHHHHHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhcChhHHHHHHHHH
Q 046621            9 QILSEKLSKLN-NSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRKGSEFVNEFWKVL   87 (213)
Q Consensus         9 ~~~~~kL~~L~-~Sq~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk~~~f~~~F~~vL   87 (213)
                      ..+...|..|+ ++..-|.++..-.-+|...|..||..+..++.++++.+||..+|++..|+.|   -|.+|...|...|
T Consensus         7 ~dy~s~ledltfnskp~i~~lt~la~En~~~a~~iv~~iE~hi~kcpp~~kL~~~y~~dsi~kn---vg~py~~~fs~~l   83 (579)
T KOG2071|consen    7 RDYQSSLEDLTFNSKPIINTLTILAEENLPFAKSIVSAIEAHIAKCPPSQKLPVMYLLDSIVKN---VGSPYTTAFSRNL   83 (579)
T ss_pred             HHHHHHHHHHhcCCcchhHHhhHhhhhcccccHHHHHHHHHHHhhCCcccccchhhhhHHHHhh---cCCcchhhhhhhH
Confidence            45667788886 8999999999999999999999999999999999999999999999999988   6778999999999


Q ss_pred             HHHHHHHhhcCChHHHHhHHHHHHHhh
Q 046621           88 PAALKHVYDNGDEYGKKAVTRLVDIWE  114 (213)
Q Consensus        88 p~~~~~v~~~~d~~~~~kv~rll~IWe  114 (213)
                      -..|..+|..+|+..+.++.+++..|.
T Consensus        84 ~a~f~~~~~~vd~r~r~~l~~~~~tw~  110 (579)
T KOG2071|consen   84 VATFICAFTKVDERTRTSLFKLRATWD  110 (579)
T ss_pred             HHHHHHHHhhccccccchhHhhHHhhc
Confidence            999999999999999999999999999

>cd00197 VHS_ENTH_ANTH VHS, ENTH and ANTH domain superfamily; composed of proteins containing a VHS, ENTH or ANTH domain

Probab=96.66  E-value=0.037  Score=42.17  Aligned_cols=92  Identities=16%  Similarity=0.164  Sum_probs=68.6

Q ss_pred             cHHHHHHHHHHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhcChhHHHHHHH--HHHHHHHHHhh--
Q 046621           21 SQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRKGSEFVNEFWK--VLPAALKHVYD--   96 (213)
Q Consensus        21 Sq~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk~~~f~~~F~~--vLp~~~~~v~~--   96 (213)
                      +...|..+..-+-.....+..++..+.+.+...+....+.-|||+.-+++||-   ..|..+|..  ++..++...+.  
T Consensus        17 ~~~~i~~i~d~~~~~~~~~~~~~~~l~kRl~~~~~~~~lkaL~lLe~lvkN~g---~~f~~~i~~~~~~~~l~~~~~~~~   93 (115)
T cd00197          17 DWPLIMEICDLINETNVGPKEAVDAIKKRINNKNPHVVLKALTLLEYCVKNCG---ERFHQEVASNDFAVELLKFDKSKL   93 (115)
T ss_pred             CHHHHHHHHHHHHCCCccHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHcc---HHHHHHHHHhHHHHHHHHhhcccc
Confidence            56667777777765656789999999999998888889999999999999954   455555544  44444433221  


Q ss_pred             ---cCChHHHHhHHHHHHHhhh
Q 046621           97 ---NGDEYGKKAVTRLVDIWEE  115 (213)
Q Consensus        97 ---~~d~~~~~kv~rll~IWee  115 (213)
                         ..+..+++++..++..|.+
T Consensus        94 ~~~~~~~~Vr~k~~~l~~~w~~  115 (115)
T cd00197          94 LGDDVSTNVREKAIELVQLWAS  115 (115)
T ss_pred             ccCCCChHHHHHHHHHHHHHhC
Confidence               2357889999999999964

The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It is located at the N-termini of proteins involved in intracellular membrane trafficking. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. VHS, ENTH and ANTH domains are structurally similar and are composed of a superhelix of eight alpha helices. ENTH adnd ANTH (E/ANTH) domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membra

>PF00790 VHS: VHS domain; InterPro: IPR002014 The VHS domain is a ~140 residues long domain, whose name is derived from its occurrence in VPS-27, Hrs and STAM

Probab=95.36  E-value=0.22  Score=39.41  Aligned_cols=91  Identities=16%  Similarity=0.223  Sum_probs=63.8

Q ss_pred             HHHHHHHHHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhcChhHHHHH--HHHHHHHHHHHhhcCCh
Q 046621           23 QSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRKGSEFVNEF--WKVLPAALKHVYDNGDE  100 (213)
Q Consensus        23 ~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk~~~f~~~F--~~vLp~~~~~v~~~~d~  100 (213)
                      +.|-.+..-+-.....+++.+..+.+.|...++...+.-|.|++-++.||-.   .|..++  ..++-.+...+......
T Consensus        24 ~~~l~icD~i~~~~~~~kea~~~l~krl~~~~~~vq~~aL~lld~lvkNcg~---~f~~ev~~~~fl~~l~~l~~~~~~~  100 (140)
T PF00790_consen   24 SLILEICDLINSSPDGAKEAARALRKRLKHGNPNVQLLALTLLDALVKNCGP---RFHREVASKEFLDELVKLIKSKKTD  100 (140)
T ss_dssp             HHHHHHHHHHHTSTTHHHHHHHHHHHHHTTSSHHHHHHHHHHHHHHHHHSHH---HHHHHHTSHHHHHHHHHHHHHTTTH
T ss_pred             HHHHHHHHHHHcCCccHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHcCCH---HHHHHHhHHHHHHHHHHHHccCCCC
Confidence            4566666666666678899999999999998888888889999999999743   333332  11333333333332232


Q ss_pred             H---HHHhHHHHHHHhhhC
Q 046621          101 Y---GKKAVTRLVDIWEER  116 (213)
Q Consensus       101 ~---~~~kv~rll~IWeeR  116 (213)
                      .   +++++..+|.-|.+.
T Consensus       101 ~~~~Vk~k~l~ll~~W~~~  119 (140)
T PF00790_consen  101 PETPVKEKILELLQEWAEA  119 (140)
T ss_dssp             HHSHHHHHHHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHHHHHH
Confidence            2   899999999999954

Based on regions surrounding the domain, VHS-proteins can be divided into 4 groups []: STAM/EAST/Hbp which all share the domain composition VHS-SH3-ITAM and carry one or two ubiquitin-interacting motifs Proteins with a FYVE domain (IPR000306 from INTERPRO) C-terminal to VHS which also carry one or two ubiquitin-interacting motifs GGA proteins with a domain composition VHS-GAT (GGA and Tom1) homology domain VHS domain alone or in combination with domains other than those listed above The VHS domain is always found at the N- terminus of proteins suggesting that such topology is important for function. The domain is considered to have a general membrane targeting/cargo recognition role in vesicular trafficking []. Resolution of the crystal structure of the VHS domain of Drosophila Hrs and human Tom1 revealed that it consists of eight helices arranged in a double-layer superhelix []. The existence of conserved patches of residues on the domain surface suggests that VHS domains may be involved in protein-protein recognition and docking. Overall, sequence similarity is low (approx 25%) amongst domain family members.; GO: 0006886 intracellular protein transport; PDB: 1X5B_A 2L0T_B 1DVP_A 3LDZ_C 3ZYQ_A 4AVX_A 3G2U_A 3G2W_A 1UJJ_A 3G2V_A ....

>cd03561 VHS VHS domain family; The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule)

Probab=94.51  E-value=0.71  Score=36.25  Aligned_cols=95  Identities=16%  Similarity=0.147  Sum_probs=67.0

Q ss_pred             HHHHHHHHHHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhcChhHHHHHH--HHHHHHHHHHhh--c
Q 046621           22 QQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRKGSEFVNEFW--KVLPAALKHVYD--N   97 (213)
Q Consensus        22 q~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk~~~f~~~F~--~vLp~~~~~v~~--~   97 (213)
                      -+.|-.+..-+-.....++..+..+.+.|...++...+.-|+|+.-++.||-..   |..++.  .+|-+++..+..  .
T Consensus        18 ~~~il~icd~I~~~~~~~k~a~raL~krl~~~n~~vql~AL~lLd~~vkNcg~~---f~~~i~s~~fl~~l~~l~~~~~~   94 (133)
T cd03561          18 WALNLELCDLINLKPNGPKEAARAIRKKIKYGNPHVQLLALTLLELLVKNCGKP---FHLQVADKEFLLELVKIAKNSPK   94 (133)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCChH---HHHHHhhHHHHHHHHHHhCCCCC
Confidence            344555555555555688999999999999888888888899999999997543   333222  234443333333  3


Q ss_pred             CChHHHHhHHHHHHHhhhCcccCC
Q 046621           98 GDEYGKKAVTRLVDIWEERKVFGS  121 (213)
Q Consensus        98 ~d~~~~~kv~rll~IWeeR~Vf~~  121 (213)
                      .++.+++++..++.-|.+  .|+.
T Consensus        95 ~~~~Vk~kil~ll~~W~~--~f~~  116 (133)
T cd03561          95 YDPKVREKALELILAWSE--SFGG  116 (133)
T ss_pred             CCHHHHHHHHHHHHHHHH--HhcC
Confidence            578999999999999995  5554

It has a superhelical structure similar to that of the ARM (Armadillo) repeats and is present at the N-termini of proteins involved in intracellular membrane trafficking. There are four general groups of VHS domain containing proteins based on their association with other domains. The first group consists of proteins of the STAM/EAST/Hbp family which has the domain composition VHS-SH3-ITAM. The second consists of proteins with a FYVE domain C-terminal to VHS. The third consists of GGA proteins with a domain composition VHS-GAT (GGA and TOM)-GAE (gamma-adaptin ear) domain. The fourth consists of proteins with a VHS domain alone or with domains other than those mentioned above. In GGA proteins, VHS domains are involved in cargo recognition in trans-Golgi, thereby having a general me

>smart00288 VHS Domain present in VPS-27, Hrs and STAM

Probab=93.77  E-value=1.2  Score=35.10  Aligned_cols=90  Identities=19%  Similarity=0.208  Sum_probs=60.5

Q ss_pred             HHHHHHHHHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhcChhHHHHHHH--HHHHHHHHHhhcCC-
Q 046621           23 QSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRKGSEFVNEFWK--VLPAALKHVYDNGD-   99 (213)
Q Consensus        23 ~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk~~~f~~~F~~--vLp~~~~~v~~~~d-   99 (213)
                      +.|-.+..-+-.....++..+..+.+.|...++...+.-|-|+..++.||-   ..|..++..  ++..+...+....+ 
T Consensus        19 ~~~l~icD~i~~~~~~~k~a~r~l~krl~~~n~~v~l~AL~lLe~~vkNcg---~~f~~ev~s~~fl~~L~~l~~~~~~~   95 (133)
T smart00288       19 ELILEICDLINSTPDGPKDAVRLLKKRLNNKNPHVALLALTLLDACVKNCG---SKFHLEVASKEFLNELVKLIKPKYPL   95 (133)
T ss_pred             HHHHHHHHHHhCCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCC---HHHHHHHHhHHHHHHHHHHHcCCCCc
Confidence            444555555545555689999999999998777778888999999999974   333333321  23333333222222 


Q ss_pred             hHHHHhHHHHHHHhhh
Q 046621          100 EYGKKAVTRLVDIWEE  115 (213)
Q Consensus       100 ~~~~~kv~rll~IWee  115 (213)
                      +.+++++..++.-|.+
T Consensus        96 ~~Vk~kil~li~~W~~  111 (133)
T smart00288       96 PLVKKRILELIQEWAD  111 (133)
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            3489999999999995

Unpublished observations. Domain of unknown function.

>cd03569 VHS_Hrs_Vps27p VHS domain family, Hrs and Vps27p subfamily; composed of Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and its yeast homolog Vps27p (vacuolar protein sorting)

Probab=93.35  E-value=1.6  Score=34.92  Aligned_cols=106  Identities=18%  Similarity=0.267  Sum_probs=68.3

Q ss_pred             HHHHHhhccC---cH---HHHHHHHHHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhc-ChhH-HHH
Q 046621           11 LSEKLSKLNN---SQ---QSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRK-GSEF-VNE   82 (213)
Q Consensus        11 ~~~kL~~L~~---Sq---~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk-~~~f-~~~   82 (213)
                      |.+.+.+.++   +.   +.|-.+..-+-.....+++.+..+.+.|...++...+.-|-|+.-++.||-.+ ..++ ...
T Consensus         5 ~~~~I~kATs~~l~~~dw~~ileicD~In~~~~~~k~a~ral~krl~~~n~~vql~AL~LLe~~vkNCG~~fh~evas~~   84 (142)
T cd03569           5 FDELIEKATSELLGEPDLASILEICDMIRSKDVQPKYAMRALKKRLLSKNPNVQLYALLLLESCVKNCGTHFHDEVASRE   84 (142)
T ss_pred             HHHHHHHHcCcccCccCHHHHHHHHHHHhCCCCCHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHHCCHHHHHHHhhHH
Confidence            4455555543   22   33344555554555678999999999998877777777799999999998543 1111 112


Q ss_pred             HHHHHHHHHHHHhhcCChHHHHhHHHHHHHhhhCcccCC
Q 046621           83 FWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGS  121 (213)
Q Consensus        83 F~~vLp~~~~~v~~~~d~~~~~kv~rll~IWeeR~Vf~~  121 (213)
                      |-..|..++..   ..++.+++++..++.-|.+  .|..
T Consensus        85 fl~~l~~l~~~---~~~~~Vk~kil~li~~W~~--~f~~  118 (142)
T cd03569          85 FMDELKDLIKT---TKNEEVRQKILELIQAWAL--AFRN  118 (142)
T ss_pred             HHHHHHHHHcc---cCCHHHHHHHHHHHHHHHH--HhCC
Confidence            22222222222   4578999999999999994  5654

The VHS domain, an essential part of Hrs/Vps27p, has a superhelical structure similar to the structure of ARM (Armadillo) repeats and is present at the N-termini of proteins. Hrs also contains a FYVE (Fab1p, YOTB, Vac1p, and EEA1) zinc finger domain C-terminal to VHS, as well as two coiled-coil domains. Hrs has been proposed to play a role in at least three vesicle trafficking events: exocytosis, endocytosis, and endosome to lysosome trafficking. Hrs is involved in promoting rapid recycling of endocytosed signaling receptors to the plasma membrane.

>cd03568 VHS_STAM VHS domain family, STAM subfamily; members include STAM (Signal Transducing Adaptor Molecule), EAST (EGFR-associated protein with SH3 and TAM domains) and Hbp (Hrs-binding protein)

Probab=91.81  E-value=3.3  Score=33.25  Aligned_cols=90  Identities=17%  Similarity=0.195  Sum_probs=61.6

Q ss_pred             HHHHHHHHHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhcChhHHHHHH--HHHHHHHHHHhhcCCh
Q 046621           23 QSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRKGSEFVNEFW--KVLPAALKHVYDNGDE  100 (213)
Q Consensus        23 ~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk~~~f~~~F~--~vLp~~~~~v~~~~d~  100 (213)
                      +.|-.+..-+-.....++..+.++.+.+....+...+.-|-|+..+++||-..   |..++.  .++..+...+....++
T Consensus        19 ~~il~icD~I~~~~~~~k~a~ral~KRl~~~n~~v~l~AL~LLe~~vkNCG~~---fh~evask~Fl~eL~kl~~~~~~~   95 (144)
T cd03568          19 GLILDVCDKVKSDENGAKDCLKAIMKRLNHKDPNVQLRALTLLDACAENCGKR---FHQEVASRDFTQELKKLINDRVHP   95 (144)
T ss_pred             HHHHHHHHHHhcCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCCHH---HHHHHhhHHHHHHHHHHhcccCCH
Confidence            34445555555566678999999999998777777777788999999997643   222221  1333333333222578


Q ss_pred             HHHHhHHHHHHHhhh
Q 046621          101 YGKKAVTRLVDIWEE  115 (213)
Q Consensus       101 ~~~~kv~rll~IWee  115 (213)
                      .++.++..++.-|.+
T Consensus        96 ~Vk~kil~li~~W~~  110 (144)
T cd03568          96 TVKEKLREVVKQWAD  110 (144)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            999999999999983

Collectively, they are referred to as STAM. All STAMs have at their N-termini a VHS domain, which is involved in cytokine-mediated intracellular signal transduction and has a superhelical structure similar to the structure of ARM (Armadillo) repeats, followed by a SH3 (Src homology 3) domain, a well-established protein-protein interaction domain. At the C-termini of most vertebrate STAMS, an ITAM (Immunoreceptor Tyrosine-based Activation) motif is present, which mediates the binding of HRS (hepatocyte growth factor-regulated tyrosine kinase substrate) in endocytic and exocytic machineries.

>cd03567 VHS_GGA VHS domain family, GGA subfamily; GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) comprise a subfamily of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins

Probab=91.17  E-value=4.5  Score=32.32  Aligned_cols=91  Identities=18%  Similarity=0.211  Sum_probs=59.8

Q ss_pred             HHHHHHHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhcChhHHHHHHH--HHHHHHHHHhh-----c
Q 046621           25 IESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRKGSEFVNEFWK--VLPAALKHVYD-----N   97 (213)
Q Consensus        25 Iqs~s~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk~~~f~~~F~~--vLp~~~~~v~~-----~   97 (213)
                      |-.+..-+-.....+...+..+.+.+..-++...|.-|-|+.-+++||-..   |..++..  +|.++++.+..     .
T Consensus        22 ileicD~In~~~~~~k~a~rai~krl~~~n~~v~l~AL~LLe~~vkNCG~~---fh~evas~~Fl~el~kl~~~k~~~~~   98 (139)
T cd03567          22 IQAFCEQINKEPEGPQLAVRLLAHKIQSPQEKEALQALTVLEACMKNCGER---FHSEVGKFRFLNELIKLVSPKYLGSR   98 (139)
T ss_pred             HHHHHHHHHcCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCHH---HHHHHHhHHHHHHHHHHhccccCCCC
Confidence            334444444444566888999999998766666777789999999997543   3222221  33333333321     2


Q ss_pred             CChHHHHhHHHHHHHhhhCcccC
Q 046621           98 GDEYGKKAVTRLVDIWEERKVFG  120 (213)
Q Consensus        98 ~d~~~~~kv~rll~IWeeR~Vf~  120 (213)
                      .++.+++++..++.-|.+  -|+
T Consensus        99 ~~~~Vk~kil~li~~W~~--~f~  119 (139)
T cd03567          99 TSEKVKTKIIELLYSWTL--ELP  119 (139)
T ss_pred             CCHHHHHHHHHHHHHHHH--Hhc
Confidence            468999999999999994  454

The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (gamma-adaptin ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the trans-Golgi network and the endosomal system.

>KOG1087 consensus Cytosolic sorting protein GGA2/TOM1 [Intracellular trafficking, secretion, and vesicular transport]

Probab=82.89  E-value=9.3  Score=36.65  Aligned_cols=83  Identities=18%  Similarity=0.249  Sum_probs=58.9

Q ss_pred             HHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhcChhHHHHH--HHHHHHHHHHHhhc-CChHHHHhH
Q 046621           30 RWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRKGSEFVNEF--WKVLPAALKHVYDN-GDEYGKKAV  106 (213)
Q Consensus        30 ~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk~~~f~~~F--~~vLp~~~~~v~~~-~d~~~~~kv  106 (213)
                      ..|=.-...++++|..+.+.+......-.+--|+|+.-++.||-.   .|-..+  ..+|.+++..+... .+..++++|
T Consensus        27 D~IN~~~~~~~eAvralkKRi~~k~s~vq~lALtlLE~cvkNCG~---~fh~~Va~k~fL~emVk~~k~~~~~~~Vr~ki  103 (470)
T KOG1087|consen   27 DLINSTEGGPKEAVRALKKRLNSKNSKVQLLALTLLETCVKNCGY---SFHLQVASKEFLNEMVKRPKNKPRDLKVREKI  103 (470)
T ss_pred             HHHhcCccCcHHHHHHHHHHhccCCcHHHHHHHHHHHHHHHhhhH---HHHHHHHHHHHHHHHHhccccCCcchhHHHHH
Confidence            333334456789999999999865554445556777777777643   333333  34788888888776 688999999


Q ss_pred             HHHHHHhhh
Q 046621          107 TRLVDIWEE  115 (213)
Q Consensus       107 ~rll~IWee  115 (213)
                      .-+|+-|.+
T Consensus       104 L~LI~~W~~  112 (470)
T KOG1087|consen  104 LELIDTWQQ  112 (470)
T ss_pred             HHHHHHHHH
Confidence            999999994

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	213
4fu3_A	135	Cid Of Human Rprd1b Length = 135		4e-27
4hfg_A	135	Cid Of Human Rprd1b Length = 135		1e-26
4flb_A	132	Cid Of Human Rprd2 Length = 132		9e-14
2km4_A	142	Solution Structure Of Rtt103 Ctd Interacting Domain		3e-08

>pdb|4FU3|A Chain A, Cid Of Human Rprd1b Length = 135

Iteration: 1
 Score =  117 bits (294), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 56/116 (48%), Positives = 78/116 (67%)
Query: 5   AFDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYL 64
           +F    L +KLS+L+NSQQS+++LS W I HRK A  IV  W +    ++  ++++FLYL
Sbjct: 3   SFSESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLYL 62
Query: 65  ANDILQNSRRKGSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFG 120
           AND++QNS+RKG EF  EF  VL  A  HV    DE  KK + RL++IW+ER V+G
Sbjct: 63  ANDVIQNSKRKGPEFTREFESVLVDAFSHVAREADEGCKKPLERLLNIWQERSVYG 118

>pdb|4HFG|A Chain A, Cid Of Human Rprd1b Length = 135

Iteration: 1
 Score =  116 bits (290), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 60/133 (45%), Positives = 82/133 (61%), Gaps = 1/133 (0%)
Query: 5   AFDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYL 64
           +F    L +KLS+L+NSQ S+++LS W I HRK A  IV  W +    ++  ++++FLYL
Sbjct: 3   SFSESALEKKLSELSNSQHSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLYL 62
Query: 65  ANDILQNSRRKGSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGSRG- 123
           AND++QNS+RKG EF  EF  VL  A  HV    DE  KK + RL++IW+ER V+G    
Sbjct: 63  ANDVIQNSKRKGPEFTREFESVLVDAFSHVAREADEGCKKPLERLLNIWQERSVYGGEFI 122
Query: 124 QGLKDEMLGKNPP 136
           Q LK  M     P
Sbjct: 123 QQLKLSMEDSKSP 135

>pdb|4FLB|A Chain A, Cid Of Human Rprd2 Length = 132

Iteration: 1
 Score = 73.6 bits (179), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 42/110 (38%), Positives = 58/110 (52%), Gaps = 4/110 (3%)
Query: 11  LSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQ 70
           L  K   + N+ +SI+ LS WCI ++K    IV  W K    S    R++  YLAND++Q
Sbjct: 10  LDRKFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSAYPHRLNLFYLANDVIQ 69
Query: 71  NSRRKGSEFVNE-FWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVF 119
           N +RK +    E F  VLP A   V D       K+V R+  IWE+R V+
Sbjct: 70  NCKRKNAIIFRESFADVLPEAAALVKDPS---VSKSVERIFKIWEDRNVY 116

>pdb|2KM4|A Chain A, Solution Structure Of Rtt103 Ctd Interacting Domain Length = 142

Iteration: 1
 Score = 54.7 bits (130), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 35/119 (29%), Positives = 63/119 (52%), Gaps = 3/119 (2%)
Query: 5   AFDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSF--NSSQKEQRVSFL 62
           AF  +  + KL+ L +SQ+SI S S+W +   + A ++ E W +     S    +++  L
Sbjct: 2   AFSSEQFTTKLNTLEDSQESISSASKWLLLQYRDAPKVAEMWKEYMLRPSVNTRRKLLGL 61
Query: 63  YLANDILQNSR-RKGSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFG 120
           YL N ++Q ++ +K  +F + F KV    L  +        KK ++R+V+I +ER +F 
Sbjct: 62  YLMNHVVQQAKGQKIIQFQDSFGKVAAEVLGRINQEFPRDLKKKLSRVVNILKERNIFS 120

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	213
4fld_A	135	Regulation of nuclear PRE-mRNA domain-containing 1	2e-46
2km4_A	142	Regulator of TY1 transposition protein 103; CTD-in	5e-42
4flb_A	132	Regulation of nuclear PRE-mRNA domain-containing;	7e-41
3d9j_A	145	RNA-binding protein 16; SCAF8, RNA polymerase II C	3e-30
1sz9_A	144	PCF11 protein; RNA polymerase II CTD interacting d	3e-23
3clj_A	157	Protein NRD1; CTD-interacting domain, nucleus, pho	5e-15
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-04

>2km4_A Regulator of TY1 transposition protein 103; CTD-interacting domain, RNA polymerase II binding protein, phosphoprotein; NMR {Saccharomyces cerevisiae} PDB: 2l0i_A* Length = 142

 Score =  138 bits (348), Expect = 5e-42
 Identities = 35/121 (28%), Positives = 64/121 (52%), Gaps = 3/121 (2%)

Query: 5   AFDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSF--NSSQKEQRVSFL 62
           AF  +  + KL+ L +SQ+SI S S+W +   + A ++ E W +     S    +++  L
Sbjct: 2   AFSSEQFTTKLNTLEDSQESISSASKWLLLQYRDAPKVAEMWKEYMLRPSVNTRRKLLGL 61

Query: 63  YLANDILQNSR-RKGSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGS 121
           YL N ++Q ++ +K  +F + F KV    L  +        KK ++R+V+I +ER +F  
Sbjct: 62  YLMNHVVQQAKGQKIIQFQDSFGKVAAEVLGRINQEFPRDLKKKLSRVVNILKERNIFSK 121

Query: 122 R 122
           +
Sbjct: 122 Q 122

>4flb_A Regulation of nuclear PRE-mRNA domain-containing; structural genomics consortium, SGC, protein binding; 1.80A {Homo sapiens} Length = 132

 Score =  135 bits (340), Expect = 7e-41
 Identities = 43/132 (32%), Positives = 62/132 (46%), Gaps = 5/132 (3%)

Query: 3   NEAFDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFL 62
           +       L  K   + N+ +SI+ LS WCI ++K    IV  W K    S    R++  
Sbjct: 2   SAGALESSLDRKFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSAYPHRLNLF 61

Query: 63  YLANDILQNSRRKG-SEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGS 121
           YLAND++QN +RK    F   F  VLP A   V    D    K+V R+  IWE+R V+  
Sbjct: 62  YLANDVIQNCKRKNAIIFRESFADVLPEAAALVK---DPSVSKSVERIFKIWEDRNVYPE 118

Query: 122 RG-QGLKDEMLG 132
                L++ +  
Sbjct: 119 EMIVALREALST 130

>3d9j_A RNA-binding protein 16; SCAF8, RNA polymerase II CTD interacting domain, arm repeats phospho-CTD, phosphoprotein, transcription; 1.60A {Homo sapiens} PDB: 3d9k_A* 3d9l_A* 3d9m_A* 3d9n_A* 3d9p_A* 3d9i_A 3d9o_A* 2diw_A Length = 145

 Score =  107 bits (269), Expect = 3e-30
 Identities = 28/138 (20%), Positives = 62/138 (44%), Gaps = 6/138 (4%)

Query: 4   EAFDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLY 63
           + F+ ++ S    K   S+  +  +++  I   K  K +V++ +K     + E +V  LY
Sbjct: 5   KTFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLY 64

Query: 64  LANDILQNSRRKGSE----FVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVF 119
           + + I++ SR +  +    F   F   + +  +++Y    +   K + R++++W++  VF
Sbjct: 65  VIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSK-IVRVLNLWQKNNVF 123

Query: 120 GSRG-QGLKDEMLGKNPP 136
            S   Q L D        
Sbjct: 124 KSEIIQPLLDMAAALEHH 141

>1sz9_A PCF11 protein; RNA polymerase II CTD interacting domain, arm repeats, transcription; 2.10A {Saccharomyces cerevisiae} SCOP: a.118.9.4 PDB: 1sza_A* 2bf0_X Length = 144

 Score = 89.7 bits (222), Expect = 3e-23
 Identities = 21/110 (19%), Positives = 41/110 (37%), Gaps = 4/110 (3%)

Query: 13  EKLSKLN-NSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQN 71
             L +L  NS+  I +L++    +   A+  V+  +        +Q++   Y  + I +N
Sbjct: 14  SILEELTFNSRPIITTLTKLAEENISCAQYFVDAIESRIEKCMPKQKLYAFYALDSICKN 73

Query: 72  SRRKGSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGS 121
               GS +   F + L    K  Y   D   +  +  +  +W      G 
Sbjct: 74  V---GSPYTIYFSRNLFNLYKRTYLLVDNTTRTKLINMFKLWLNPNDTGL 120

>3clj_A Protein NRD1; CTD-interacting domain, nucleus, phosphoprotein, RNA polymer binding protein, RNA binding protein; 2.10A {Saccharomyces cerevisiae} Length = 157

 Score = 68.7 bits (167), Expect = 5e-15
 Identities = 22/135 (16%), Positives = 47/135 (34%), Gaps = 14/135 (10%)

Query: 1   MSNEAFDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVS 60
           M  + F   + S K  K   S   I+ L+ + + H     +I+              ++ 
Sbjct: 1   MDFQNFVATLESFKDLKSGISGSRIKKLTTYALDHIDIESKIISLIIDYSRLCPDSHKLG 60

Query: 61  FLYLANDILQNSRRKG--------------SEFVNEFWKVLPAALKHVYDNGDEYGKKAV 106
            LY+ + I +    +               +  +N   +V+   L       ++  K+ +
Sbjct: 61  SLYIIDSIGRAYLDETRSNSNSSSNKPGTCAHAINTLGEVIQELLSDAIAKSNQDHKEKI 120

Query: 107 TRLVDIWEERKVFGS 121
             L+DIW+   +F  
Sbjct: 121 RMLLDIWDRSGLFQK 135

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 40.6 bits (94), Expect = 3e-04
 Identities = 37/238 (15%), Positives = 78/238 (32%), Gaps = 68/238 (28%)

Query: 9   QILS-EKLSKLNNSQQSIESLSR--WCITHRKKAKQIVETWDKSFNSSQKEQRVSFLY-- 63
            ILS E++  +  S+ ++    R  W +    K +++V    + F          FL   
Sbjct: 44  SILSKEEIDHIIMSKDAVSGTLRLFWTL--LSKQEEMV----QKFVEEVLRINYKFLMSP 97

Query: 64  LANDILQNSRRKGSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERK------ 117
           +  +  Q S      ++ +           +Y++   + K  V+RL    + R+      
Sbjct: 98  IKTEQRQPSMMT-RMYIEQ--------RDRLYNDNQVFAKYNVSRLQPYLKLRQALLELR 148

Query: 118 ------VFGSRGQG--------LKDE-MLGKNPPPVP-ASNGRSSNPIKIVK-------- 153
                 + G  G G             +  K    +   +    ++P  +++        
Sbjct: 149 PAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQ 208

Query: 154 -------RDANSVRIKLAVGALPEKILTAFQS--------VLDEHPNEEV--ALN-NC 193
                  R  +S  IKL + ++  ++    +S        VL    N +   A N +C
Sbjct: 209 IDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSC 266

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	213
2km4_A	142	Regulator of TY1 transposition protein 103; CTD-in	100.0
4fu3_A	135	Regulation of nuclear PRE-mRNA domain-containing 1	100.0
4flb_A	132	Regulation of nuclear PRE-mRNA domain-containing;	100.0
3d9j_A	145	RNA-binding protein 16; SCAF8, RNA polymerase II C	99.95
1sz9_A	144	PCF11 protein; RNA polymerase II CTD interacting d	99.94
3clj_A	157	Protein NRD1; CTD-interacting domain, nucleus, pho	99.68
1x5b_A	163	Signal transducing adaptor molecule 2; VHS domain,	94.41
3ldz_A	140	STAM-1, signal transducing adapter molecule 1; ubi	91.65
1dvp_A	220	HRS, hepatocyte growth factor-regulated tyrosine k	90.48
3zyq_A	226	Hepatocyte growth factor-regulated tyrosine kinas	90.48
1mhq_A	148	ADP-ribosylation factor binding protein GGA2; supe	89.66
3g2s_A	149	C-terminal fragment of sortilin-related receptor;	89.53
1juq_A	171	ADP-ribosylation factor binding protein GGA3; prot	88.65
1elk_A	157	Target of MYB1; superhelix of helices, endocytosis	86.5
4fla_A	152	Regulation of nuclear PRE-mRNA domain-containing 1	83.65

>2km4_A Regulator of TY1 transposition protein 103; CTD-interacting domain, RNA polymerase II binding protein, phosphoprotein; NMR {Saccharomyces cerevisiae} PDB: 2l0i_A*

Probab=100.00  E-value=1.7e-38  Score=253.56  Aligned_cols=129  Identities=26%  Similarity=0.454  Sum_probs=122.2

Q ss_pred             CCCHHHHHHHHhhccCcHHHHHHHHHHHHhchhchHHHHHHHHHHhccC--cccchhHHHHHhHHHHHHhhhc-ChhHHH
Q 046621            5 AFDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSS--QKEQRVSFLYLANDILQNSRRK-GSEFVN   81 (213)
Q Consensus         5 ~F~~~~~~~kL~~L~~Sq~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~a--~~~~KL~lLYLaNDIlqnskrk-~~~f~~   81 (213)
                      +||++.|.++|++||+||+||+++|.|||+|+++++.||++|.++|.++  ++++||++|||+|||+|||+++ +++|++
T Consensus         2 ~fs~~~l~~kL~~L~~sq~sIq~~s~W~l~h~~~a~~iv~~~~~~l~~~~~~~~kKL~~lYL~NDVlqnsk~k~~~~f~~   81 (142)
T 2km4_A            2 AFSSEQFTTKLNTLEDSQESISSASKWLLLQYRDAPKVAEMWKEYMLRPSVNTRRKLLGLYLMNHVVQQAKGQKIIQFQD   81 (142)
T ss_dssp             CCCHHHHHHHHHTCCSCHHHHHHHHHHHHTCGGGHHHHHHHHHHHHTSSSSCHHHHHHHHHHHHHHHHHHGGGTCCHHHH
T ss_pred             CCCHHHHHHHHHhccccHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhcCCCccceehhhhhHHHHHHHHhhcCchHHHH
Confidence            7999999999999999999999999999999999999999999999986  6799999999999999999987 589999


Q ss_pred             HHHHHHHHHHHHHhhcCChHHHHhHHHHHHHhhhCcccCCCc-cchhhhhhCC
Q 046621           82 EFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGSRG-QGLKDEMLGK  133 (213)
Q Consensus        82 ~F~~vLp~~~~~v~~~~d~~~~~kv~rll~IWeeR~Vf~~~~-~~L~~~~lg~  133 (213)
                      +|+++||++|.+++..+|++.+++|.|||+||++|+||++++ .+|+..+.|.
T Consensus        82 ~F~~~L~~~~~~~~~~~~~~~~~kv~rvl~iWeer~vf~~~~i~~L~~~l~~~  134 (142)
T 2km4_A           82 SFGKVAAEVLGRINQEFPRDLKKKLSRVVNILKERNIFSKQVVNDIERSLAAA  134 (142)
T ss_dssp             HHHHTHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTCSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhhccCCcCHHHHHHHHHHHHhH
Confidence            999999999999999889999999999999999999999996 7788777663

>4fu3_A Regulation of nuclear PRE-mRNA domain-containing 1B; structural genomics consortium, SGC, domain swapping, transc; HET: MSE; 1.90A {Homo sapiens} PDB: 4fld_A*

Probab=100.00  E-value=2.3e-38  Score=249.24  Aligned_cols=134  Identities=46%  Similarity=0.753  Sum_probs=122.3

Q ss_pred             CCCCCHHHHHHHHhhccCcHHHHHHHHHHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhcChhHHHH
Q 046621            3 NEAFDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRKGSEFVNE   82 (213)
Q Consensus         3 ~~~F~~~~~~~kL~~L~~Sq~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk~~~f~~~   82 (213)
                      +++|+++.|.++|+.||+||+||++++.||++|+++++.||++|.++|.++++++||++|||+|||+|||++++++|+.+
T Consensus         1 ~ssf~~~~l~~~L~~L~~s~~sI~~~s~w~l~~~~~a~~iv~~i~~~l~~~~~~~KL~~LYLindIl~ns~~~~~~y~~~   80 (135)
T 4fu3_A            1 GSSFSESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLYLANDVIQNSKRKGPEFTRE   80 (135)
T ss_dssp             --CCCHHHHHHHHHHCCSSTTHHHHHHHHHHHTGGGHHHHHHHHHHHHHHSCTTTHHHHHHHHHHHHHHHTTTCSHHHHH
T ss_pred             CCCCCHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHhcCHHHHHH
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhcCChHHHHhHHHHHHHhhhCcccCCCc-cchhhhhhCCCCC
Q 046621           83 FWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGSRG-QGLKDEMLGKNPP  136 (213)
Q Consensus        83 F~~vLp~~~~~v~~~~d~~~~~kv~rll~IWeeR~Vf~~~~-~~L~~~~lg~~p~  136 (213)
                      |+++||.+|.+++..+++..+++|.|||++|++|+||++++ .+|+..+.+..||
T Consensus        81 f~~~l~~~~~~~~~~~~~~~k~kl~kll~iW~~r~vf~~~~i~~L~~~l~~~~~P  135 (135)
T 4fu3_A           81 FESVLVDAFSHVAREADEGCKKPLERLLNIWQERSVYGGEFIQQLKLSMEDSKSP  135 (135)
T ss_dssp             HHTTHHHHHHHHHHHHHTTSSHHHHHHHHHHHHTTSSCHHHHHHHHHTC------
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhcCCCCcCHHHHHHHHHHHhCCCCC
Confidence            99999999999998778889999999999999999999996 8888888776554

>4flb_A Regulation of nuclear PRE-mRNA domain-containing; structural genomics consortium, SGC, protein binding; 1.80A {Homo sapiens}

Probab=100.00  E-value=1.3e-34  Score=227.35  Aligned_cols=125  Identities=34%  Similarity=0.576  Sum_probs=116.4

Q ss_pred             CCCCHHHHHHHHhhccCcHHHHHHHHHHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhcC-hhHHHH
Q 046621            4 EAFDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRKG-SEFVNE   82 (213)
Q Consensus         4 ~~F~~~~~~~kL~~L~~Sq~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk~-~~f~~~   82 (213)
                      ++|.++.|.++|++||+||+||++++.||++|+++++.||++|.++|.++++++||++|||+|||+|||++++ +.|..+
T Consensus         3 ~~~~e~~l~~~L~~L~~s~~sI~~~s~w~l~h~~~a~~Iv~~i~~~l~~~~~~~KL~~LYL~ndIl~ns~~~~~~~f~~~   82 (132)
T 4flb_A            3 AGALESSLDRKFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSAYPHRLNLFYLANDVIQNCKRKNAIIFRES   82 (132)
T ss_dssp             HHHHHHHHHHHHHHCCSSHHHHHHHHHHHHHTGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTTTTTCTHHHHH
T ss_pred             chHHHHHHHHHHHHCcccHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHhcccChHHHHHH
Confidence            4678899999999999999999999999999999999999999999999999999999999999999999886 789999


Q ss_pred             HHHHHHHHHHHHhhcCChHHHHhHHHHHHHhhhCcccCCCc-cchhhhhh
Q 046621           83 FWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGSRG-QGLKDEML  131 (213)
Q Consensus        83 F~~vLp~~~~~v~~~~d~~~~~kv~rll~IWeeR~Vf~~~~-~~L~~~~l  131 (213)
                      |+++||.+|.+++   +++.++++.|||+||++|+||++++ .+|++.+-
T Consensus        83 f~~~l~~~~~~~~---~~~~~~kl~~ll~iW~~r~vf~~~~i~~L~~~L~  129 (132)
T 4flb_A           83 FADVLPEAAALVK---DPSVSKSVERIFKIWEDRNVYPEEMIVALREALS  129 (132)
T ss_dssp             HHTTHHHHHHTTC---STTTHHHHHHHHHHHHHHTSSCHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhC---CHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHh
Confidence            9999999999875   6788999999999999999999996 77776544

>3d9j_A RNA-binding protein 16; SCAF8, RNA polymerase II CTD interacting domain, arm repeats phospho-CTD, phosphoprotein, transcription; 1.60A {Homo sapiens} PDB: 3d9k_A* 3d9l_A* 3d9m_A* 3d9n_A* 3d9p_A* 3d9i_A 3d9o_A* 2diw_A

Probab=99.95  E-value=5.9e-28  Score=193.26  Aligned_cols=123  Identities=22%  Similarity=0.345  Sum_probs=113.6

Q ss_pred             HHHHHHHHhhc-----cCcHHHHHHHHHHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhcCh----h
Q 046621            8 GQILSEKLSKL-----NNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRKGS----E   78 (213)
Q Consensus         8 ~~~~~~kL~~L-----~~Sq~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk~~----~   78 (213)
                      .+.|+.+|+.|     ++|+.+|++++.||++|+++++.||++|.+++.++++++||++|||+|||+||+++++.    +
T Consensus         4 v~~f~~~L~~L~~~k~~~S~~~I~~LT~~a~~~~~~~~~IV~~~~~~i~k~~~~~KL~~LYL~DsIvrn~~~k~~~~~~~   83 (145)
T 3d9j_A            4 VKTFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRHQFGQEKDV   83 (145)
T ss_dssp             HHHHHHHHHGGGGSCSSCCHHHHHHHHHHHHHTGGGHHHHHHHHHHHHHHSCGGGHHHHHHHHHHHHHHHHHHHCTTTCS
T ss_pred             HHHHHHHHHHHHhccCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccceeehhhhhHHHHHHhhhhcCCcccc
Confidence            47899999999     56899999999999999999999999999999999999999999999999999998743    7


Q ss_pred             HHHHHHHHHHHHHHHHhhcCChHHHHhHHHHHHHhhhCcccCCCc-cchhhhhh
Q 046621           79 FVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGSRG-QGLKDEML  131 (213)
Q Consensus        79 f~~~F~~vLp~~~~~v~~~~d~~~~~kv~rll~IWeeR~Vf~~~~-~~L~~~~l  131 (213)
                      |...|+++||.+|.++|.. ++..+.++.||++||++|+||+++. ..+++.+.
T Consensus        84 f~~~F~~~L~~~f~~~~~~-~~~~r~kl~rLl~iW~~r~vF~~~~l~~l~~~l~  136 (145)
T 3d9j_A           84 FAPRFSNNIISTFQNLYRC-PGDDKSKIVRVLNLWQKNNVFKSEIIQPLLDMAA  136 (145)
T ss_dssp             HHHHHHHHHHHHHHHHTSS-CGGGHHHHHHHHHHHHHTTSSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhC-CHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhc
Confidence            9999999999999999965 5899999999999999999999996 66776554

>1sz9_A PCF11 protein; RNA polymerase II CTD interacting domain, arm repeats, transcription; 2.10A {Saccharomyces cerevisiae} SCOP: a.118.9.4 PDB: 1sza_A* 2bf0_X

Probab=99.94  E-value=1.2e-26  Score=185.51  Aligned_cols=120  Identities=18%  Similarity=0.292  Sum_probs=112.7

Q ss_pred             HHHHHHHhhcc-CcHHHHHHHHHHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhcChhHHHHHHHHH
Q 046621            9 QILSEKLSKLN-NSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRKGSEFVNEFWKVL   87 (213)
Q Consensus         9 ~~~~~kL~~L~-~Sq~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk~~~f~~~F~~vL   87 (213)
                      +.|.++|+.|+ +|+.+|++++.||++|.++++.||++|.+++.++++.+||++|||+|||++|+   |.+|...|+++|
T Consensus        10 ~~f~~~L~~L~~nSk~~I~~LT~~a~~~~~~a~~Iv~~i~~~i~k~~p~~KL~~LYL~DsIvkN~---g~~y~~~F~~~l   86 (144)
T 1sz9_A           10 KDFNSILEELTFNSRPIITTLTKLAEENISCAQYFVDAIESRIEKCMPKQKLYAFYALDSICKNV---GSPYTIYFSRNL   86 (144)
T ss_dssp             HHHHHHHTTCSSCCHHHHHHHHHHHHHTGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHT---CTTHHHHHHTTH
T ss_pred             HHHHHHHHHhccccHhHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHhhHHHHHHHHHHHHHhc---cchHHHHHHHHH
Confidence            67999999999 99999999999999999999999999999999999999999999999999995   467999999999


Q ss_pred             HHHHHHHhhcCChHHHHhHHHHHHHhhhC-----cccCCCc-cchhhhhh
Q 046621           88 PAALKHVYDNGDEYGKKAVTRLVDIWEER-----KVFGSRG-QGLKDEML  131 (213)
Q Consensus        88 p~~~~~v~~~~d~~~~~kv~rll~IWeeR-----~Vf~~~~-~~L~~~~l  131 (213)
                      +.+|.++|..+|+.++.++.||+++|++|     +||++++ ..++..+.
T Consensus        87 ~~~f~~~~~~~d~~~r~k~~rL~~~W~~~~~~~~~vF~~~~l~~i~~~l~  136 (144)
T 1sz9_A           87 FNLYKRTYLLVDNTTRTKLINMFKLWLNPNDTGLPLFEGSALEKIEQFLI  136 (144)
T ss_dssp             HHHHHHHHHTSCHHHHHHHHHHHHHHTSGGGCSSCSSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHHHhCcccCCCCCCCHHHHHHHHHHHH
Confidence            99999999999999999999999999999     9999997 66665544

>3clj_A Protein NRD1; CTD-interacting domain, nucleus, phosphoprotein, RNA polymer binding protein, RNA binding protein; 2.10A {Saccharomyces cerevisiae}

Probab=99.68  E-value=6.1e-16  Score=125.02  Aligned_cols=122  Identities=16%  Similarity=0.270  Sum_probs=108.0

Q ss_pred             HHHHHHHHhhcc-----CcHHHHHHHHHHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhc----C--
Q 046621            8 GQILSEKLSKLN-----NSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRK----G--   76 (213)
Q Consensus         8 ~~~~~~kL~~L~-----~Sq~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk----~--   76 (213)
                      .+.|+.-|+.|.     .|..-|.+++.||+.|.++++.||+.+.+++.++++.+||..|||+++|+.+++.+    |  
T Consensus         3 v~ef~~~L~sL~~lkp~iS~skI~~LT~~A~~nv~~~~~iv~~l~~~ikk~p~~hKL~~LYVvDSIvR~~~~~~~k~g~~   82 (157)
T 3clj_A            3 FQNFVATLESFKDLKSGISGSRIKKLTTYALDHIDIESKIISLIIDYSRLCPDSHKLGSLYIIDSIGRAYLDETRSNSNS   82 (157)
T ss_dssp             HHHHHHHHHGGGGCSSSCCHHHHHHHHHHHHHTGGGHHHHHHHHHHHHHHSCGGGHHHHHHHHHHHHHHHHHHHHTCCC-
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHhCCCcceeeeeeehHHHHHHHHHHHHhcCCc
Confidence            678999999883     68999999999999999999999999999999999999999999999999998841    1  


Q ss_pred             -----hhH---HHHHHHHHHHHHHHHhhcCChHHHHhHHHHHHHhhhCcccCCCc-cchhhh
Q 046621           77 -----SEF---VNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGSRG-QGLKDE  129 (213)
Q Consensus        77 -----~~f---~~~F~~vLp~~~~~v~~~~d~~~~~kv~rll~IWeeR~Vf~~~~-~~L~~~  129 (213)
                           ..|   +.-|...+|..+..++..+++..+.++.+||+||+.+++|++++ +.+++.
T Consensus        83 ~~a~~gt~a~~v~~~~e~i~~l~~~~~~~~~~~~k~Ki~klldiW~k~~~Fp~e~i~~i~~~  144 (157)
T 3clj_A           83 SSNKPGTCAHAINTLGEVIQELLSDAIAKSNQDHKEKIRMLLDIWDRSGLFQKSYLNAIRSK  144 (157)
T ss_dssp             ---STTSHHHHHHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTTTTTSCCTTTTSH
T ss_pred             cCCCCccHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHccCCCCCHHHHHHHHHH
Confidence                 125   45678899999999998889999999999999999999999996 666654

>1x5b_A Signal transducing adaptor molecule 2; VHS domain, ubiquitin binding, STAM2, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2l0t_B

Probab=94.41  E-value=0.46  Score=37.69  Aligned_cols=108  Identities=17%  Similarity=0.190  Sum_probs=74.8

Q ss_pred             CCHHHHHHHHhhccCc------HHHHHHHHHHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhc-C--
Q 046621            6 FDGQILSEKLSKLNNS------QQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRK-G--   76 (213)
Q Consensus         6 F~~~~~~~kL~~L~~S------q~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk-~--   76 (213)
                      |....|.+.+.+.++.      =..|-.+..-+-.....+++.+.++.+.|..-.+...+.-|-|++-+++||-.. .  
T Consensus        11 ~~~~p~~~~IekATs~~~~~~Dw~~~leicD~I~~~~~~~keA~ral~krl~~~n~~vql~AL~LLd~~vkNcG~~Fh~e   90 (163)
T 1x5b_A           11 FTANPFEQDVEKATNEYNTTEDWSLIMDICDKVGSTPNGAKDCLKAIMKRVNHKVPHVALQALTLLGACVANCGKIFHLE   90 (163)
T ss_dssp             CCCCTTHHHHHHHTCTTCSSCCHHHHHHHHHHHHHSSSHHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             cCCChHHHHHHHHcCCCCCCcCHHHHHHHHHHHhCCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhHHHHHH
Confidence            5555566666666642      345555666665656678999999999998766777788899999999997533 1  


Q ss_pred             ---hhHHHHHHHHHHHHHHHHhhcCChHHHHhHHHHHHHhhhCcccCCC
Q 046621           77 ---SEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGSR  122 (213)
Q Consensus        77 ---~~f~~~F~~vLp~~~~~v~~~~d~~~~~kv~rll~IWeeR~Vf~~~  122 (213)
                         .+|.+++.+++       ....++.+++++..++.-|.+  -|..+
T Consensus        91 vas~~Fl~el~~l~-------~~~~~~~Vk~kil~li~~W~~--~f~~~  130 (163)
T 1x5b_A           91 VCSRDFATEVRAVI-------KNKAHPKVCEKLKSLMVEWSE--EFQKD  130 (163)
T ss_dssp             HTSHHHHHHHHHHH-------HTTCCHHHHHHHHHHHHHHHH--HTTTC
T ss_pred             HhhHHHHHHHHHHH-------ccCCCHHHHHHHHHHHHHHHH--HhcCC
Confidence               24444443322       233578999999999999996  45543

>3ldz_A STAM-1, signal transducing adapter molecule 1; ubiquitin-binding, cytoplasm, UBL conjugation, endosome, membrane, protein transport, SH3 domain; 2.60A {Homo sapiens} SCOP: a.118.9.0

Probab=91.65  E-value=2.5  Score=32.45  Aligned_cols=85  Identities=16%  Similarity=0.186  Sum_probs=61.9

Q ss_pred             HHHHHHHHHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhc-----C-hhHHHHHHHHHHHHHHHHhh
Q 046621           23 QSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRK-----G-SEFVNEFWKVLPAALKHVYD   96 (213)
Q Consensus        23 ~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk-----~-~~f~~~F~~vLp~~~~~v~~   96 (213)
                      +.|-.+..-+-.....+++.+..+.+.|....+...+.-|-|+.-+++||-..     + .+|.+++...++        
T Consensus        24 ~~ileicD~I~~~~~~~k~a~rai~Krl~~~n~~~ql~AL~LLe~~vkNcG~~f~~evas~~Fl~el~~l~~--------   95 (140)
T 3ldz_A           24 GLILDICDKVGQSRTGPKDCLRSIMRRVNHKDPHVAMQALTLLGACVSNCGKIFHLEVCSRDFASEVSNVLN--------   95 (140)
T ss_dssp             HHHHHHHHHHTTSTTHHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHSCHHHHHHHSSHHHHHHHHHHHH--------
T ss_pred             HHHHHHHHHHHCCCcCHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhcCHHHHHHHhhHHHHHHHHHHhc--------
Confidence            45555656555555678999999999998766666777788999999997532     1 345555544332        


Q ss_pred             cCChHHHHhHHHHHHHhhh
Q 046621           97 NGDEYGKKAVTRLVDIWEE  115 (213)
Q Consensus        97 ~~d~~~~~kv~rll~IWee  115 (213)
                      ..++.+++++..++.-|.+
T Consensus        96 ~~~~~Vk~kil~li~~W~~  114 (140)
T 3ldz_A           96 KGHPKVCEKLKALMVEWTD  114 (140)
T ss_dssp             HSCHHHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHHHH
Confidence            2478999999999999996

>1dvp_A HRS, hepatocyte growth factor-regulated tyrosine kinase substrate; VHS, FYVE, zinc finger, superhelix, transferase; HET: CIT; 2.00A {Drosophila melanogaster} SCOP: a.118.9.2 g.50.1.1

Probab=90.48  E-value=1.9  Score=35.44  Aligned_cols=102  Identities=19%  Similarity=0.191  Sum_probs=71.8

Q ss_pred             HHHHHhhccC------cHHHHHHHHHHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhc-----C-hh
Q 046621           11 LSEKLSKLNN------SQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRK-----G-SE   78 (213)
Q Consensus        11 ~~~kL~~L~~------Sq~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk-----~-~~   78 (213)
                      |.+.+.+.++      -=..|-.+..-+-.....+++.+..+.+.|...++...+.-|.|++-++.||-..     + .+
T Consensus         6 ~~~~ie~AT~~~~~~~dw~~~leicd~i~~~~~~~k~a~r~l~krl~~~n~~~~l~aL~Lle~~vkNcG~~f~~eva~~~   85 (220)
T 1dvp_A            6 FCKNLENATSHLRLEPDWPSILLICDEINQKDVTPKNAFAAIKKKMNSPNPHSSCYSLLVLESIVKNCGAPVHEEVFTKE   85 (220)
T ss_dssp             HHHHHHHHHCTTCSSCCHHHHHHHHHHHHTTSSCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHSHHHHHHHHSSHH
T ss_pred             HHHHHHHHcCCCCCCcCHHHHHHHHHhhcCCCcCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhccCHHHHHHHHhHH
Confidence            5555655553      2344556666666556688999999999998777777788899999999997532     1 34


Q ss_pred             HHHHHHHHHHHHHHHHhhcCChHHHHhHHHHHHHhhhCcccCC
Q 046621           79 FVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGS  121 (213)
Q Consensus        79 f~~~F~~vLp~~~~~v~~~~d~~~~~kv~rll~IWeeR~Vf~~  121 (213)
                      |.+++...+.       ...++.+++++..++.-|.+-  |..
T Consensus        86 fl~~l~~l~~-------~~~~~~Vk~kil~li~~W~~~--f~~  119 (220)
T 1dvp_A           86 NCEMFSSFLE-------STPHENVRQKMLELVQTWAYA--FRS  119 (220)
T ss_dssp             HHHHHHHHHH-------HCSCHHHHHHHHHHHHHHHHH--TTT
T ss_pred             HHHHHHHHhc-------CCCcHHHHHHHHHHHHHHHHH--hcc
Confidence            5555544332       234789999999999999964  554

>3zyq_A Hepatocyte growth factor-regulated tyrosine kinas substrate; signaling; 1.48A {Homo sapiens} PDB: 4avx_A*

Probab=90.48  E-value=2.1  Score=35.47  Aligned_cols=104  Identities=15%  Similarity=0.225  Sum_probs=74.0

Q ss_pred             HHHHHHhhccC------cHHHHHHHHHHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhc-----C-h
Q 046621           10 ILSEKLSKLNN------SQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRK-----G-S   77 (213)
Q Consensus        10 ~~~~kL~~L~~------Sq~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk-----~-~   77 (213)
                      .|++.+.+.++      --+.|-.+..-+-.....+++.+..+.+.|...++...|.-|-|+.-+++||-..     . .
T Consensus         8 ~~~~~i~kAT~~~~~~~dw~~ileicD~I~~~~~~~k~a~ral~krl~~~n~~v~l~aL~LLe~~vkNcG~~f~~eias~   87 (226)
T 3zyq_A            8 TFERLLDKATSQLLLETDWESILQICDLIRQGDTQAKYAVNSIKKKVNDKNPHVALYALEVMESVVKNCGQTVHDEVANK   87 (226)
T ss_dssp             HHHHHHHHHTCTTCSSCCHHHHHHHHHHHHTTSSCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHHCHHHHHHHSSH
T ss_pred             hHHHHHHHHcCCCCCCcCHHHHHHHHHHHhCCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcchHHHHhhccH
Confidence            55566665553      2356677777776666678999999999998767777777788999999997743     1 2


Q ss_pred             hHHHHHHHHHHHHHHHHhhcCChHHHHhHHHHHHHhhhCcccCCC
Q 046621           78 EFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGSR  122 (213)
Q Consensus        78 ~f~~~F~~vLp~~~~~v~~~~d~~~~~kv~rll~IWeeR~Vf~~~  122 (213)
                      +|.+++...+       -...++.+++++..+|.-|.+  -|..+
T Consensus        88 ~fl~~l~~l~-------~~~~~~~Vk~kil~li~~W~~--~f~~~  123 (226)
T 3zyq_A           88 QTMEELKDLL-------KRQVEVNVRNKILYLIQAWAH--AFRNE  123 (226)
T ss_dssp             HHHHHHHHHH-------HHCCCHHHHHHHHHHHHHHHH--HTTTC
T ss_pred             HHHHHHHHHh-------ccCCCHHHHHHHHHHHHHHHH--HhCCC
Confidence            4555444332       234578999999999999996  35443

>1mhq_A ADP-ribosylation factor binding protein GGA2; super helix, protein transport; 2.20A {Homo sapiens} SCOP: a.118.9.2

Probab=89.66  E-value=2.5  Score=32.88  Aligned_cols=95  Identities=14%  Similarity=0.154  Sum_probs=65.8

Q ss_pred             HHHHHHHHHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhcChhHHHHH--HHHHHHHHHHHhh----
Q 046621           23 QSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRKGSEFVNEF--WKVLPAALKHVYD----   96 (213)
Q Consensus        23 ~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk~~~f~~~F--~~vLp~~~~~v~~----   96 (213)
                      +.|-.+..-+-.....++..+..+.+.|...++...+.-|-|++-+++||-.   .|..++  ..+|..+...+..    
T Consensus        20 ~~~leicD~I~~~~~~~k~a~rai~krl~~~n~~vql~AL~LLe~~vkNCG~---~fh~evas~~Fl~eL~kl~~~k~~~   96 (148)
T 1mhq_A           20 SAIQNFCEQVNTDPNGPTHAPWLLAHKIQSPQEKEALYALTVLEMCMNHCGE---KFHSEVAKFRFLNELIKVLSPKYLG   96 (148)
T ss_dssp             HHHHHHHHHHHHSSHHHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHSCH---HHHHHHTSHHHHHHHHHTTCCSTTS
T ss_pred             HHHHHHHHHHHcCCccHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHcCH---HHHHHHhhHHHHHHHHHHHccccCC
Confidence            4455666666565667899999999999877777778888999999999643   343333  2244443333321    


Q ss_pred             -cCChHHHHhHHHHHHHhhhCcccCCC
Q 046621           97 -NGDEYGKKAVTRLVDIWEERKVFGSR  122 (213)
Q Consensus        97 -~~d~~~~~kv~rll~IWeeR~Vf~~~  122 (213)
                       ..++.+++++..++.-|.+.  |..+
T Consensus        97 ~~~~~~Vk~kil~li~~W~~~--f~~~  121 (148)
T 1mhq_A           97 SWATGKVKGRVIEILFSWTVW--FPED  121 (148)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHH--CTTC
T ss_pred             CCCCHHHHHHHHHHHHHHHHH--cCCC
Confidence             23789999999999999964  6654

>3g2s_A C-terminal fragment of sortilin-related receptor; ADP-ribosylation factor binding protein GGA1, VHS, acidic- cluster dileucine signal, sorla; 1.70A {Homo sapiens} SCOP: a.118.9.2 PDB: 3g2t_A* 3g2u_A 3g2v_A* 3g2w_A 1ujk_A* 1jwf_A 1ujj_A 1jwg_A* 1py1_A*

Probab=89.53  E-value=2.8  Score=32.64  Aligned_cols=107  Identities=15%  Similarity=0.200  Sum_probs=68.6

Q ss_pred             HHHHHHhhccC---c---HHHHHHHHHHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhcChhHHHHH
Q 046621           10 ILSEKLSKLNN---S---QQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRKGSEFVNEF   83 (213)
Q Consensus        10 ~~~~kL~~L~~---S---q~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk~~~f~~~F   83 (213)
                      .|.+.+.+.++   +   =+.|-.+..-+-.....++..+..+.+.+...++...+.-|-|+.-+++||-.   .|..++
T Consensus        11 ~~~~~IekATs~~l~~~dw~~ileicD~I~~~~~~pk~a~ral~krl~~~n~~v~l~AL~LLe~cvkNCG~---~fh~ei   87 (149)
T 3g2s_A           11 TLEARINRATNPLNKELDWASINGFCEQLNEDFEGPPLATRLLAHKIQSPQEWEAIQALTVLETCMKSCGK---RFHDEV   87 (149)
T ss_dssp             CHHHHHHHHSCTTCSSCCHHHHHHHHHHGGGSSSHHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHCCH---HHHHHH
T ss_pred             cHHHHHHHHcCCCCCCcCHHHHHHHHHHHHCCCCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcCH---HHHHHH
Confidence            34555555543   2   23555555555555556889999999999876666677778899999999753   332322


Q ss_pred             --HHHHHHHHHHHhh-----cCChHHHHhHHHHHHHhhhCcccCC
Q 046621           84 --WKVLPAALKHVYD-----NGDEYGKKAVTRLVDIWEERKVFGS  121 (213)
Q Consensus        84 --~~vLp~~~~~v~~-----~~d~~~~~kv~rll~IWeeR~Vf~~  121 (213)
                        ..+|..+++.+..     ..++.+++++..++.-|.+  -|+.
T Consensus        88 as~~Fl~eL~kl~~~k~~~~~~~~~Vk~kil~li~~W~~--~f~~  130 (149)
T 3g2s_A           88 GKFRFLNELIKVVSPKYLGSRTSEKVKNKILELLYSWTV--GLPE  130 (149)
T ss_dssp             TSHHHHHHHHHHHCTTTTGGGSCHHHHHHHHHHHHHHHH--HCTT
T ss_pred             hhHHHHHHHHHHHcccccCCCCCHHHHHHHHHHHHHHHH--HhCC
Confidence              1133333333321     2478999999999999996  3554

>1juq_A ADP-ribosylation factor binding protein GGA3; protein-peptide compelx, VHS domain, DXXLL sorting signal, signaling protein; 2.20A {Homo sapiens} SCOP: a.118.9.2 PDB: 1jpl_A 1lf8_A*

Probab=88.65  E-value=3.5  Score=32.78  Aligned_cols=107  Identities=21%  Similarity=0.227  Sum_probs=71.9

Q ss_pred             HHHHHHhhccCc------HHHHHHHHHHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhc-C-----h
Q 046621           10 ILSEKLSKLNNS------QQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRK-G-----S   77 (213)
Q Consensus        10 ~~~~kL~~L~~S------q~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk-~-----~   77 (213)
                      .|.+.+.+.++.      =..|-.+..-+-.....+++.+..+.+.+...++...+.-|-|+.-+++||-.. .     .
T Consensus        13 ~~~~~IekATs~~l~~~Dw~~ileicD~I~~~~~~~k~A~ral~krl~~~n~~vql~AL~LLd~~vkNCG~~Fh~evas~   92 (171)
T 1juq_A           13 SLESWLNKATNPSNRQEDWEYIIGFCDQINKELEGPQIAVRLLAHKIQSPQEWEALQALTVLEACMKNCGRRFHNEVGKF   92 (171)
T ss_dssp             CHHHHHHHHTCTTCSSCCHHHHHHHHHHHHHSTTHHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHSHHHHHHHHTSH
T ss_pred             cHHHHHHHHcCCCCCCcCHHHHHHHHHHHHcCCccHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHcCHHHHHHHhhH
Confidence            466666666642      345556666666666678899999999998767777788889999999997533 1     2


Q ss_pred             hHHHHHHHHHHHHHHHHh--hcCChHHHHhHHHHHHHhhhCcccCCC
Q 046621           78 EFVNEFWKVLPAALKHVY--DNGDEYGKKAVTRLVDIWEERKVFGSR  122 (213)
Q Consensus        78 ~f~~~F~~vLp~~~~~v~--~~~d~~~~~kv~rll~IWeeR~Vf~~~  122 (213)
                      +|.+++...    +..-+  ...++.+++++..+|.-|.+-  |..+
T Consensus        93 ~Fl~eL~kl----~~~k~~~~~~~~~Vk~kil~li~~W~~~--f~~~  133 (171)
T 1juq_A           93 RFLNELIKV----VSPKYLGDRVSEKVKTKVIELLYSWTMA--LPEE  133 (171)
T ss_dssp             HHHHHHHHH----HCCCCCCTTSCHHHHHHHHHHHHHHHHH--CTTC
T ss_pred             HHHHHHHHH----hccccCCCCCCHHHHHHHHHHHHHHHHH--cCCC
Confidence            344443332    21111  123679999999999999964  6654

>1elk_A Target of MYB1; superhelix of helices, endocytosis/exocytosis complex; 1.50A {Homo sapiens} SCOP: a.118.9.2

Probab=86.50  E-value=5.3  Score=31.16  Aligned_cols=109  Identities=9%  Similarity=0.139  Sum_probs=69.3

Q ss_pred             CCCCCHHHHHHHHhhccC------cHHHHHHHHHHHHhchhchHHHHHHHHHHhcc-CcccchhHHHHHhHHHHHHhhhc
Q 046621            3 NEAFDGQILSEKLSKLNN------SQQSIESLSRWCITHRKKAKQIVETWDKSFNS-SQKEQRVSFLYLANDILQNSRRK   75 (213)
Q Consensus         3 ~~~F~~~~~~~kL~~L~~------Sq~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~-a~~~~KL~lLYLaNDIlqnskrk   75 (213)
                      .++|+. .+...+.+.++      -=..|-.+..-+-.....+++.+..+.+.|.. .++...+.-|-|++-+++||-  
T Consensus        10 ~~p~~s-~~~~~IekATs~~l~~~Dw~~~leicD~I~~~~~~~k~a~ral~krl~~~~n~~v~l~AL~LLd~~vkNcG--   86 (157)
T 1elk_A           10 GNPFSS-PVGQRIEKATDGSLQSEDWALNMEICDIINETEEGPKDALRAVKKRIVGNKNFHEVMLALTVLETCVKNCG--   86 (157)
T ss_dssp             SCGGGS-HHHHHHHHHTCTTCSSCCHHHHHHHHHHHHHSSSHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHSC--
T ss_pred             CCCCCc-HHHHHHHHHcCCCCCCcCHHHHHHHHHHHhCCCccHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHhC--
Confidence            445542 25555655554      23455566665555556789999999999973 455566777889999999974  


Q ss_pred             ChhHHHHHH--HHHHH-HHHHHhhc--CChHHHHhHHHHHHHhhh
Q 046621           76 GSEFVNEFW--KVLPA-ALKHVYDN--GDEYGKKAVTRLVDIWEE  115 (213)
Q Consensus        76 ~~~f~~~F~--~vLp~-~~~~v~~~--~d~~~~~kv~rll~IWee  115 (213)
                       ..|..++.  .+|.+ +++.+...  .+..+++++..++.-|.+
T Consensus        87 -~~fh~eva~~~fl~e~Lvk~~~~k~~~~~~Vk~kil~li~~W~~  130 (157)
T 1elk_A           87 -HRFHVLVASQDFVESVLVRTILPKNNPPTIVHDKVLNLIQSWAD  130 (157)
T ss_dssp             -HHHHHHHTSHHHHHHHTHHHHSTTTCCCHHHHHHHHHHHHHHHH
T ss_pred             -HHHHHHHhhHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHHHHH
Confidence             23333332  13333 23333222  245889999999999997

>4fla_A Regulation of nuclear PRE-mRNA domain-containing 1B; structural genomics consortium, SGC, transcription; 2.20A {Homo sapiens}

Probab=83.65  E-value=0.29  Score=38.73  Aligned_cols=33  Identities=15%  Similarity=0.179  Sum_probs=26.5

Q ss_pred             hcccCCChHHHHHHHHHHHhhCCChHHHHHHhH
Q 046621          162 KLAVGALPEKILTAFQSVLDEHPNEEVALNNCN  194 (213)
Q Consensus       162 ~~~~~~~~eki~~~~~~~~~~~~~e~~~~~k~~  194 (213)
                      +.+.++.++.++.+.+++.+.+++|.++|+++.
T Consensus        17 ~~~~p~~~~elik~L~~le~sassDa~vrq~Ia   49 (152)
T 4fla_A           17 QGAGPLLTEELIKALQDLENAASGDATVRQKIA   49 (152)
T ss_dssp             ------CHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHhhccccchHHHHHHHH
Confidence            455678999999999999999999999999998

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	213
d1szaa_	144	a.118.9.4 (A:) PCF11 protein {Baker's yeast (Sacch	4e-28

>d1szaa_ a.118.9.4 (A:) PCF11 protein {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 144

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ENTH/VHS domain
family: RPR domain (SMART 00582 )
domain: PCF11 protein
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  101 bits (252), Expect = 4e-28
 Identities = 19/110 (17%), Positives = 39/110 (35%), Gaps = 4/110 (3%)

Query: 13  EKLSKLN-NSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQN 71
             L +L  NS+  I +L++    +   A+  V+  +        +Q++   Y  + I +N
Sbjct: 14  SILEELTFNSRPIITTLTKLAEENISCAQYFVDAIESRIEKCMPKQKLYAFYALDSICKN 73

Query: 72  SRRKGSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGS 121
                  +   F + L    K  Y   D   +  +  +  +W      G 
Sbjct: 74  VGS---PYTIYFSRNLFNLYKRTYLLVDNTTRTKLINMFKLWLNPNDTGL 120

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	213
d1szaa_	144	PCF11 protein {Baker's yeast (Saccharomyces cerevi	99.95
d1dvpa1	145	Hrs {Fruit fly (Drosophila melanogaster) [TaxId: 7	93.11
d1ujka_	145	ADP-ribosylation factor binding protein Gga1 {Huma	91.67
d1mhqa_	143	ADP-ribosylation factor binding protein Gga2 {Huma	89.78
d1juqa_	151	ADP-ribosylation factor binding protein Gga3 {Huma	88.08
d1elka_	153	Tom1 protein {Human (Homo sapiens) [TaxId: 9606]}	84.97

>d1szaa_ a.118.9.4 (A:) PCF11 protein {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ENTH/VHS domain
family: RPR domain (SMART 00582 )
domain: PCF11 protein
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.95  E-value=9.1e-28  Score=189.86  Aligned_cols=125  Identities=17%  Similarity=0.264  Sum_probs=115.1

Q ss_pred             CHHHHHHHHhhcc-CcHHHHHHHHHHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhcChhHHHHHHH
Q 046621            7 DGQILSEKLSKLN-NSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRKGSEFVNEFWK   85 (213)
Q Consensus         7 ~~~~~~~kL~~L~-~Sq~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk~~~f~~~F~~   85 (213)
                      ..+.|...|+.|+ +++..|++|+.||++|+.+|..||++|.+++..+++++||++|||+|||+|||   +.+|..+|++
T Consensus         8 ~~~~f~~~L~~L~~ns~~~I~~Lt~~a~~~~~~a~~Iv~~i~~~i~~~~~~~KL~~LYLiddI~~n~---~~~y~~~f~~   84 (144)
T d1szaa_           8 IVKDFNSILEELTFNSRPIITTLTKLAEENISCAQYFVDAIESRIEKCMPKQKLYAFYALDSICKNV---GSPYTIYFSR   84 (144)
T ss_dssp             HHHHHHHHHTTCSSCCHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHT---CTTHHHHHHT
T ss_pred             HHHHHHHHHHHHhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCcccchhhhhhHHHHHHHh---HHHHHHHHHH
Confidence            3577999999998 79999999999999999999999999999999999999999999999999998   4579999999


Q ss_pred             HHHHHHHHHhhcCChHHHHhHHHHHHHhhhCc-----ccCCCc-cchhhhhhCCC
Q 046621           86 VLPAALKHVYDNGDEYGKKAVTRLVDIWEERK-----VFGSRG-QGLKDEMLGKN  134 (213)
Q Consensus        86 vLp~~~~~v~~~~d~~~~~kv~rll~IWeeR~-----Vf~~~~-~~L~~~~lg~~  134 (213)
                      +||.+|.++|..+++..++++.||++||++|+     ||++++ +.++..+.+..
T Consensus        85 ~l~~~f~~~y~~~~~~~r~kl~rll~iW~~r~~~~~~vFp~~~l~~ie~~L~~a~  139 (144)
T d1szaa_          85 NLFNLYKRTYLLVDNTTRTKLINMFKLWLNPNDTGLPLFEGSALEKIEQFLIKAS  139 (144)
T ss_dssp             THHHHHHHHHTTSCHHHHHHHHHHHHHHSSGGGCSSCSSCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHhccCCCCcCCCCHHHHHHHHHHHHHhH
Confidence            99999999999999999999999999999998     899997 77776665543

>d1dvpa1 a.118.9.2 (A:1-145) Hrs {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ENTH/VHS domain
family: VHS domain
domain: Hrs
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=93.11  E-value=0.36  Score=35.51  Aligned_cols=99  Identities=16%  Similarity=0.163  Sum_probs=71.5

Q ss_pred             HHHHHHhhccC------cHHHHHHHHHHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhc-C-----h
Q 046621           10 ILSEKLSKLNN------SQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRK-G-----S   77 (213)
Q Consensus        10 ~~~~kL~~L~~------Sq~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk-~-----~   77 (213)
                      .|+..+.+-|+      -=+.|-.+..-+-.....++..+.++.+.+....+...+.-|.|+.-++.||-.. .     .
T Consensus         5 ~~~~~iekAT~~~~~~~dw~~il~icD~I~~~~~~~k~a~ral~krl~~~n~~v~l~aL~LLd~~vkNcG~~f~~~i~s~   84 (145)
T d1dvpa1           5 SFCKNLENATSHLRLEPDWPSILLICDEINQKDVTPKNAFAAIKKKMNSPNPHSSCYSLLVLESIVKNCGAPVHEEVFTK   84 (145)
T ss_dssp             HHHHHHHHHHCTTCSSCCHHHHHHHHHHHHTTSSCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHSHHHHHHHHSSH
T ss_pred             hHHHHHHHHcCcCCCCCCHHHHHHHHHHHhCCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHccchHHHHHHhhH
Confidence            35555555543      3456667777676666678999999999998777778888899999999998643 1     2


Q ss_pred             hHHHHHHHHHHHHHHHHhhcCChHHHHhHHHHHHHhhh
Q 046621           78 EFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEE  115 (213)
Q Consensus        78 ~f~~~F~~vLp~~~~~v~~~~d~~~~~kv~rll~IWee  115 (213)
                      +|.+++...       +....+..+++++..++..|.+
T Consensus        85 ~fl~~l~~l-------~~~~~~~~Vk~kil~li~~W~~  115 (145)
T d1dvpa1          85 ENCEMFSSF-------LESTPHENVRQKMLELVQTWAY  115 (145)
T ss_dssp             HHHHHHHHH-------HHHCSCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHH-------hcCCCCHHHHHHHHHHHHHHHH
Confidence            444444432       2234467899999999999996

>d1ujka_ a.118.9.2 (A:) ADP-ribosylation factor binding protein Gga1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ENTH/VHS domain
family: VHS domain
domain: ADP-ribosylation factor binding protein Gga1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.67  E-value=0.48  Score=34.94  Aligned_cols=110  Identities=15%  Similarity=0.180  Sum_probs=69.2

Q ss_pred             CCHHHHHHHHhhccC---c---HHHHHHHHHHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhcChhH
Q 046621            6 FDGQILSEKLSKLNN---S---QQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRKGSEF   79 (213)
Q Consensus         6 F~~~~~~~kL~~L~~---S---q~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk~~~f   79 (213)
                      +.+..|+..+...++   +   -+.|-.+..-+-.....++..+.++.+.+....+...+.-|.|+.-++.||-   +.|
T Consensus         4 ~~~~~~e~~iekAT~~~l~~~dw~~ileicD~I~~~~~~~k~a~r~l~krl~~~~~~~~l~aL~LLe~~vkNCG---~~f   80 (145)
T d1ujka_           4 MEPETLEARINRATNPLNKELDWASINGFCEQLNEDFEGPPLATRLLAHKIQSPQEWEAIQALTVLETCMKSCG---KRF   80 (145)
T ss_dssp             GSTTSHHHHHHHHTCTTCSSCCHHHHHHHHHHHTSSTTHHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHTSCC---HHH
T ss_pred             CCcchHHHHHHHHcCCCCCCcCHHHHHHHHHHHhCCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHh---HHH
Confidence            345566777776663   2   3444455555544555688999999999987666666777888888888863   333


Q ss_pred             HHHHH--HHHHHHHHHHh-----hcCChHHHHhHHHHHHHhhhCcccC
Q 046621           80 VNEFW--KVLPAALKHVY-----DNGDEYGKKAVTRLVDIWEERKVFG  120 (213)
Q Consensus        80 ~~~F~--~vLp~~~~~v~-----~~~d~~~~~kv~rll~IWeeR~Vf~  120 (213)
                      ..++.  .++..+...+.     ...+..+++++..++..|.+  -|+
T Consensus        81 ~~evas~~Fl~~L~kli~~k~~~~~~~~~Vk~kil~li~~W~~--~fp  126 (145)
T d1ujka_          81 HDEVGKFRFLNELIKVVSPKYLGSRTSEKVKNKILELLYSWTV--GLP  126 (145)
T ss_dssp             HHHHTSHHHHHHHHHHHCTTTTGGGSCHHHHHHHHHHHHHHHH--HCT
T ss_pred             HHHHhhHHHHHHHHHHHhhccCCCCCcHHHHHHHHHHHHHHHH--HCC
Confidence            33321  12222222222     12467889999999999985  454

>d1mhqa_ a.118.9.2 (A:) ADP-ribosylation factor binding protein Gga2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ENTH/VHS domain
family: VHS domain
domain: ADP-ribosylation factor binding protein Gga2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.78  E-value=1.1  Score=32.66  Aligned_cols=96  Identities=14%  Similarity=0.119  Sum_probs=64.5

Q ss_pred             HHHHHHHHHHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhcChhHHHHHH--HHHHHHHHHHh----
Q 046621           22 QQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRKGSEFVNEFW--KVLPAALKHVY----   95 (213)
Q Consensus        22 q~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk~~~f~~~F~--~vLp~~~~~v~----   95 (213)
                      =+.|-.+..-+-.....+...+.++.+.+....+...+.-|-|+..++.||-.   .|..++.  .++..+...+.    
T Consensus        19 w~~il~icD~I~~~~~~~k~a~ral~krl~~~n~~~~l~aL~LLe~~vkNcG~---~fh~evask~Fl~~l~~li~~k~~   95 (143)
T d1mhqa_          19 WSAIQNFCEQVNTDPNGPTHAPWLLAHKIQSPQEKEALYALTVLEMCMNHCGE---KFHSEVAKFRFLNELIKVLSPKYL   95 (143)
T ss_dssp             HHHHHHHHHHHHHSSHHHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHSCH---HHHHHHTSHHHHHHHHHTTCCSTT
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCH---HHHHHHhhHHHHHHHHHHHccccC
Confidence            34555666666666667889999999999877777778888899999998643   3333321  12222222222    


Q ss_pred             -hcCChHHHHhHHHHHHHhhhCcccCCC
Q 046621           96 -DNGDEYGKKAVTRLVDIWEERKVFGSR  122 (213)
Q Consensus        96 -~~~d~~~~~kv~rll~IWeeR~Vf~~~  122 (213)
                       ...++.+++++..++.-|.+  -|+.+
T Consensus        96 ~~~~~~~Vk~kil~li~~Wa~--~f~~~  121 (143)
T d1mhqa_          96 GSWATGKVKGRVIEILFSWTV--WFPED  121 (143)
T ss_dssp             SCCCCHHHHHHHHHHHHHHHH--HCTTC
T ss_pred             CCCCCHHHHHHHHHHHHHHHH--HcCCC
Confidence             12467899999999999986  36654

>d1juqa_ a.118.9.2 (A:) ADP-ribosylation factor binding protein Gga3 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ENTH/VHS domain
family: VHS domain
domain: ADP-ribosylation factor binding protein Gga3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.08  E-value=1.5  Score=32.23  Aligned_cols=94  Identities=19%  Similarity=0.212  Sum_probs=59.5

Q ss_pred             HHHHHHHHHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhcChhHHHHH--HHHHHHHHHHHhh----
Q 046621           23 QSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRKGSEFVNEF--WKVLPAALKHVYD----   96 (213)
Q Consensus        23 ~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk~~~f~~~F--~~vLp~~~~~v~~----   96 (213)
                      +.|-.+..-+-.....++..+..+.+.+....+...+.-|-|+.-+++||-.+   |..++  ..++..+...+..    
T Consensus        21 ~~ileicD~In~~~~~~k~a~rai~krl~~~~~~~~l~aL~LLe~~vkNCG~~---F~~evask~Fl~~l~kli~~k~~~   97 (151)
T d1juqa_          21 EYIIGFCDQINKELEGPQIAVRLLAHKIQSPQEWEALQALTVLEACMKNCGRR---FHNEVGKFRFLNELIKVVSPKYLG   97 (151)
T ss_dssp             HHHHHHHHHHHHSTTHHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHSHHH---HHHHHTSHHHHHHHHHHHCCCCCC
T ss_pred             HHHHHHHHHHhcCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHccHH---HHHHHhhHHHHHHHHHHHcccCCC
Confidence            34445555555555568899999999998766666666677888888886433   32222  1123233333321    


Q ss_pred             -cCChHHHHhHHHHHHHhhhCcccCC
Q 046621           97 -NGDEYGKKAVTRLVDIWEERKVFGS  121 (213)
Q Consensus        97 -~~d~~~~~kv~rll~IWeeR~Vf~~  121 (213)
                       ..++.+++++..++..|.+  -|+.
T Consensus        98 ~~~~~~Vk~kil~ll~~Wa~--~f~~  121 (151)
T d1juqa_          98 DRVSEKVKTKVIELLYSWTM--ALPE  121 (151)
T ss_dssp             TTSCHHHHHHHHHHHHHHHH--HCTT
T ss_pred             CcccHHHHHHHHHHHHHHHH--Hccc
Confidence             1356799999999999986  4553

>d1elka_ a.118.9.2 (A:) Tom1 protein {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ENTH/VHS domain
family: VHS domain
domain: Tom1 protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.97  E-value=5.5  Score=29.02  Aligned_cols=110  Identities=9%  Similarity=0.147  Sum_probs=68.1

Q ss_pred             CCCCCCHHHHHHHHhhccC------cHHHHHHHHHHHHhchhchHHHHHHHHHHhcc-CcccchhHHHHHhHHHHHHhhh
Q 046621            2 SNEAFDGQILSEKLSKLNN------SQQSIESLSRWCITHRKKAKQIVETWDKSFNS-SQKEQRVSFLYLANDILQNSRR   74 (213)
Q Consensus         2 ~~~~F~~~~~~~kL~~L~~------Sq~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~-a~~~~KL~lLYLaNDIlqnskr   74 (213)
                      +.++|+ ..+.+.+.+.++      -=+.|-.+..-+-.....++..+.++.+.+.. .++...+.-|.|+.-++.||-.
T Consensus         5 ~~~p~~-t~~~~~vekAT~~~l~~~dw~~il~icD~In~~~~~~k~a~ral~krL~~~~n~~v~l~aL~LLe~~vkNCG~   83 (153)
T d1elka_           5 LGNPFS-SPVGQRIEKATDGSLQSEDWALNMEICDIINETEEGPKDALRAVKKRIVGNKNFHEVMLALTVLETCVKNCGH   83 (153)
T ss_dssp             CSCGGG-SHHHHHHHHHTCTTCSSCCHHHHHHHHHHHHHSSSHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHSCH
T ss_pred             cCCCCC-ChHHHHHHHHcCCCCCcccHHHHHHHHHHHhCCCcCHHHHHHHHHHHHccCCCHHHHHHHHHHHHHHHHHccH
Confidence            455664 224555555542      24456666666655566789999999999854 3455666678899999999743


Q ss_pred             cChhHHHHH--HHHHHHH-HHHHhhc--CChHHHHhHHHHHHHhhh
Q 046621           75 KGSEFVNEF--WKVLPAA-LKHVYDN--GDEYGKKAVTRLVDIWEE  115 (213)
Q Consensus        75 k~~~f~~~F--~~vLp~~-~~~v~~~--~d~~~~~kv~rll~IWee  115 (213)
                      +   |..++  ..+|-++ +..+...  .+..+++++..++.-|.+
T Consensus        84 ~---fh~evas~~Fl~~ll~~~~~~~~~~~~~Vk~kil~li~~W~~  126 (153)
T d1elka_          84 R---FHVLVASQDFVESVLVRTILPKNNPPTIVHDKVLNLIQSWAD  126 (153)
T ss_dssp             H---HHHHHTSHHHHHHHTHHHHSTTTCCCHHHHHHHHHHHHHHHH
T ss_pred             H---HHHHHhhHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHHHHH
Confidence            2   22222  1122222 2333322  245689999999999986